Step-by-Step Guide 6 Steps

How to File GST Returns in India (GSTR-1, GSTR-3B, GSTR-9)

Complete guide on how to file GST returns in India in 2026. Covers GSTR-1 for outward supplies, GSTR-3B monthly summary, GSTR-9 annual return, due dates, late fees, interest, input tax credit reconciliation, and step by step filing process on the GST portal.

D
Dhanush Prabha
10 min read
Quick Overview
Estimated Cost ₹1000
Time Required 1 to 2 Hours per Return
Total Steps 6 Steps
What You'll Need

Documents Required

  • GSTIN (GST Identification Number) of the registered business
  • Complete record of all sales invoices issued during the return period
  • Complete record of all purchase invoices received during the return period
  • Bank statements showing tax payments and business transactions
  • HSN or SAC codes for all goods and services supplied
  • Credit and debit notes issued or received during the period
  • Previous period GSTR-2B auto populated data for input tax credit matching
  • Details of advance payments received and adjusted during the period

Tools & Prerequisites

  • Active GST portal account at gst.gov.in with valid login credentials
  • Digital Signature Certificate (DSC) or Electronic Verification Code (EVC) for return signing
  • Accounting software such as Tally, Zoho Books, or ClearTax for invoice data preparation
  • GST Offline Utility Tool for bulk upload of invoices in JSON format
  • Chartered Accountant or GST practitioner for professional filing assistance

Filing GST returns correctly and on time is one of the most important ongoing compliance obligations for every business registered under the Goods and Services Tax regime in India. Whether you run a Private Limited Company, an LLP, a sole proprietorship, or any other business entity, you must file periodic GST returns reporting your sales, purchases, tax collected, and input tax credit claimed. This guide covers the complete GST return filing process for 2026, including GSTR-1, GSTR-3B, GSTR-9, due dates, late fees, and reconciliation best practices.

The GST return filing system in India has been continuously simplified since its introduction in 2017. Today, most regular businesses need to file just two returns per month (GSTR-1 and GSTR-3B) and one annual return (GSTR-9). Small businesses with turnover up to 5 crore rupees can opt for the quarterly filing scheme (QRMP). This guide walks you through every step, from organizing your invoices to filing the annual return and handling reconciliation.

Overview of GST Returns in India

The GST return filing framework requires registered taxpayers to report their business transactions periodically to the government. Each return type serves a specific purpose in the compliance chain.

Types of GST Returns for Regular Taxpayers

GST Returns Overview for Regular Taxpayers (2026)
Return Purpose Frequency Due Date
GSTR-1 Details of outward supplies (sales) Monthly or Quarterly 11th of following month (13th for quarterly)
GSTR-3B Summary return with tax payment Monthly or Quarterly 20th of following month (22nd/24th for quarterly)
GSTR-9 Annual return consolidating all data Annual 31 December of following year
GSTR-9C Reconciliation statement (turnover above 5 crore) Annual 31 December of following year
If your aggregate annual turnover is up to 5 crore rupees, you can opt for the QRMP (Quarterly Return Monthly Payment) scheme. Under QRMP, you file GSTR-1 and GSTR-3B quarterly instead of monthly, though you still pay tax monthly using the PMT-06 challan by the 25th of each month.

Who Needs to File GST Returns

Every person or business registered under GST must file returns, even if there were no transactions during the period. This includes:

  • Regular taxpayers with active GST registration
  • Composition scheme dealers who file GSTR-4 annually and CMP-08 quarterly
  • E-commerce operators who file GSTR-8 for TCS collection
  • Input Service Distributors (ISD) who file GSTR-6
  • Non-resident taxable persons who file GSTR-5
  • TDS deductors under GST who file GSTR-7

Failure to file returns blocks your ability to file subsequent returns, prevents E-way bill generation, and can lead to suo motu cancellation of your GST registration after 6 months of continuous non-filing.

Step 1: Organize Your Invoice Data

The foundation of accurate GST return filing is well organized invoice data. Before filing any return, ensure your sales and purchase records are complete and categorized correctly.

Outward Supply (Sales) Organization

  • B2B invoices: All sales to registered GST dealers with recipient GSTIN, invoice number, date, HSN/SAC code, taxable value, and tax amount (CGST + SGST or IGST)
  • B2C Large: Inter-state sales above 2.5 lakh rupees to unregistered persons, reported at invoice level
  • B2C Small: All other sales to unregistered persons, reported as consolidated state-wise totals by tax rate
  • Export invoices: Supplies to recipients outside India with shipping bill number and port code
  • Credit and debit notes: Any adjustments to previously issued invoices
  • Nil-rated and exempt supplies: Supplies on which no GST is charged

Inward Supply (Purchase) Organization

  • Regular purchases: All purchase invoices with supplier GSTIN and tax details for ITC claims
  • Reverse charge purchases: Supplies on which you must pay GST under RCM (legal services, GTA, etc.)
  • Import of goods: Bill of Entry details for claiming IGST paid at customs
  • Import of services: Invoices for services received from outside India
Manual data organization is time consuming and error prone. Use accounting software like Tally Prime, Zoho Books, ClearTax, or Busy Accounting that automatically categorizes invoices, calculates tax, and generates GSTR-1 and GSTR-3B data in the format required by the GST portal. This saves hours of work every month and significantly reduces filing errors.

Step 2: File GSTR-1 (Outward Supply Details)

GSTR-1 is the return where you declare all your outward supplies (sales) made during the return period. The data you report in GSTR-1 populates your buyers' GSTR-2B, enabling them to claim input tax credit.

GSTR-1 Filing Process

  1. Log into the GST portal at gst.gov.in
  2. Navigate to Returns Dashboard and select the return period
  3. Click on GSTR-1 and choose Prepare Online or Upload JSON
  4. Enter or upload invoices in the relevant tables:
    • Table 4A: B2B invoices to registered persons
    • Table 5A: B2C Large inter-state invoices
    • Table 7: B2C Small consolidated summaries
    • Table 6A: Export invoices
    • Table 9: Credit and debit notes
    • Table 8: Nil-rated and exempt supplies
    • Table 12: HSN wise summary of outward supplies
  5. Click Generate Summary to preview the complete GSTR-1
  6. Verify all figures against your accounting records
  7. Click Submit to freeze the data (no further edits possible)
  8. Click File GSTR-1 and sign using DSC or EVC
Once GSTR-1 is filed, it cannot be revised. Any errors must be corrected through the Amendment Tables (9A, 9B, 9C) in the next month's GSTR-1. Double check all invoice details, especially GSTINs and tax amounts, before submitting.

Step 3: Reconcile Input Tax Credit Using GSTR-2B

Before filing GSTR-3B, download your GSTR-2B statement from the GST portal. This auto-generated statement shows all the ITC available to you based on your suppliers' GSTR-1 filings.

How to Reconcile GSTR-2B

  1. Download GSTR-2B from the Returns section of the GST portal (available from the 14th of each month)
  2. Compare each invoice in GSTR-2B against your purchase records
  3. Identify matching invoices where the supplier's GSTR-1 data matches your books
  4. Flag missing invoices where you have purchase records but the supplier has not filed GSTR-1
  5. Identify excess credits that appear in GSTR-2B but are not in your records
  6. Check for mismatches in tax amounts, invoice numbers, or dates
  7. Only claim ITC that is reflected in GSTR-2B to avoid future reversals
As per the current rules, you can claim ITC only to the extent of the amount appearing in your GSTR-2B plus 5 percent of the eligible ITC in GSTR-2B. Any ITC claimed beyond this threshold will be auto-reversed. This makes GSTR-2B reconciliation mandatory before filing GSTR-3B every month.

Step 4: File GSTR-3B (Monthly Summary and Tax Payment)

GSTR-3B is the summary return where you declare your total output tax liability, claim input tax credit, and pay the net tax due. It is the most critical return because this is where actual tax payment happens.

GSTR-3B Filing Process

  1. Log into the GST portal and select GSTR-3B for the return period
  2. The system auto-populates some values from your GSTR-1 data
  3. Fill in or verify the following tables:
    • Table 3.1: Outward supplies (taxable, zero-rated, nil-rated, exempt, and non-GST)
    • Table 3.2: Inter-state supplies to unregistered persons and composition dealers
    • Table 4: Eligible ITC (from GSTR-2B reconciliation)
    • Table 5: Exempt, nil-rated, and non-GST inward supplies
  4. Review the tax computation showing output tax minus ITC and net payable
  5. If there is a tax liability, click Create Challan and pay through net banking, NEFT/RTGS, or credit ledger
  6. After payment confirmation, click File GSTR-3B using DSC or EVC
When paying tax through GSTR-3B, the system follows a specific offset order. IGST credit is first used to offset IGST liability, then CGST, then SGST. CGST credit offsets CGST first, then IGST. SGST credit offsets SGST first, then IGST. Understanding this order helps optimize your tax cash flow.

Step 5: File GSTR-9 Annual Return

At the end of each financial year, every registered taxpayer (with turnover above 2 crore rupees) must file GSTR-9, the annual return that consolidates all monthly or quarterly returns.

GSTR-9 Structure

GSTR-9 Annual Return Parts and Details
Part Content
Part I Basic details (GSTIN, legal name, financial year)
Part II Details of outward and inward supplies as declared in monthly returns
Part III Details of ITC declared and ITC reversed during the year
Part IV Details of tax paid including through cash and credit ledger
Part V Transactions of previous year reported in current year returns
Part VI Other information including HSN summary, late fees, and demands

GSTR-9 must be filed by December 31 of the year following the financial year. For example, GSTR-9 for FY 2025-26 is due by December 31, 2026.

GST Return Due Dates and Filing Calendar

Use this comprehensive calendar to track all your GST filing deadlines throughout the year.

Monthly Filing Due Dates

Monthly GST Return Due Dates for Regular Taxpayers
Return Filing Frequency Due Date
GSTR-1 (Monthly) Monthly 11th of the following month
GSTR-3B (Monthly) Monthly 20th of the following month
GSTR-1 (Quarterly under QRMP) Quarterly 13th of the month following the quarter
GSTR-3B (Quarterly under QRMP) Quarterly 22nd or 24th of the month following the quarter
PMT-06 (Monthly tax payment under QRMP) Monthly 25th of the following month
IFF (Invoice Furnishing Facility under QRMP) Month 1 and 2 of quarter 13th of the following month

Annual Filing Due Dates

Annual GST Return Due Dates
Return Applicable To Due Date
GSTR-9 Regular taxpayers (turnover above 2 crore) 31 December of following year
GSTR-9C Taxpayers with turnover above 5 crore 31 December of following year
GSTR-4 Composition scheme dealers 30 April of following year

Late Fees and Interest for GST Returns

Understanding the financial consequences of late filing helps prioritize timely compliance.

Late Fee Structure

GST Late Fee Schedule (2026)
Return Late Fee (Per Day) Maximum Cap
GSTR-1 / GSTR-3B (Regular) 50 rupees (25 CGST + 25 SGST) 5,000 to 10,000 rupees per return
GSTR-1 / GSTR-3B (Nil) 20 rupees (10 CGST + 10 SGST) 500 rupees per return
GSTR-9 (Annual) 200 rupees (100 CGST + 100 SGST) 0.50% of turnover in the state

Interest on Late Tax Payment

  • 18 percent per annum: On tax paid after the due date (calculated on net cash liability)
  • 24 percent per annum: On excess ITC wrongly claimed and utilized, or on tax collected but not deposited
If you miss the GSTR-3B filing for one month, you cannot file returns for subsequent months. This creates a cascading effect where late fees and interest pile up for each unfiled month. Additionally, your E-way bill generation gets blocked, effectively halting goods transportation for your business. File on time every month without exception.

Input Tax Credit: Rules and Best Practices

Input tax credit is the mechanism that prevents cascading taxation and is the backbone of the GST system. Claiming ITC correctly is critical for both cash flow optimization and compliance.

Conditions for Claiming ITC

  • You must possess a valid tax invoice or debit note issued by the supplier
  • You must have actually received the goods or services
  • The supplier must have filed their GSTR-1 and the invoice must appear in your GSTR-2B
  • You must have paid the tax to the government (for RCM supplies)
  • You must file your GSTR-3B return claiming the ITC
  • You must have paid the supplier within 180 days of the invoice date (otherwise ITC must be reversed)

Blocked Credits Under Section 17(5)

ITC is not available for certain categories of expenses regardless of business use:

  • Motor vehicles and conveyances (except when used for transportation of goods or passengers, or for training)
  • Food and beverages, outdoor catering, beauty treatment, health services, and cosmetic surgery
  • Membership of clubs, health and fitness centres
  • Travel benefits extended to employees on vacation (LTC)
  • Works contract services for construction of immovable property (except plant and machinery)
  • Goods or services used for personal consumption
  • Goods lost, stolen, destroyed, written off, or disposed of as free samples

Common GST Return Filing Mistakes to Avoid

Avoiding these common errors can save your business from notices, penalties, and audit issues.

  1. Mismatch between GSTR-1 and GSTR-3B: Ensure the total taxable value and tax amount in GSTR-1 matches GSTR-3B for every period. The annual return flags all mismatches
  2. Claiming ITC not reflected in GSTR-2B: Only claim ITC that appears in your auto-populated GSTR-2B statement. Excess claims will be reversed with interest
  3. Incorrect place of supply: Applying CGST+SGST instead of IGST (or vice versa) based on wrong place of supply determination creates inter-state complications
  4. Missing credit and debit notes: Credit notes must be declared in GSTR-1 by November 30 of the following year. Missing this deadline means you cannot reduce your tax liability
  5. Wrong HSN or SAC codes: Incorrect classification can lead to wrong tax rate application and demands from the GST department
  6. Not filing nil returns: Even with zero transactions, filing nil returns is mandatory. Non-filing leads to late fees and potential registration cancellation
  7. Ignoring reverse charge supplies: Services from advocates, GTA, and directors must be reported under RCM in GSTR-3B Table 3.1(d)
  8. Not reconciling monthly: Leaving reconciliation to year end makes it exponentially harder to identify and fix discrepancies

GST Return Filing for Different Business Types

For Private Limited Companies and LLPs

Private Limited Companies and LLPs typically have monthly filing obligations as their turnover often exceeds the QRMP threshold. These entities must integrate GST return filing with their broader compliance calendar including ROC annual filings, income tax returns, and secretarial compliances.

For Sole Proprietorships and Small Businesses

Sole proprietors and small businesses with turnover up to 5 crore rupees should consider opting for the QRMP scheme to reduce filing frequency. Those with turnover up to 1.5 crore rupees may also evaluate the composition scheme which simplifies compliance further with a single annual return.

For Exporters

Businesses involved in import and export must carefully manage their export invoices in GSTR-1 Table 6A, file LUT applications for tax-free exports, and track IGST refund claims or accumulated ITC refunds through Form RFD-01.

Tools and Software for GST Return Filing

Investing in the right tools saves hours of manual work and reduces errors significantly.

  • Tally Prime: Most widely used in India, supports GSTR-1, GSTR-3B, and GSTR-9 with direct portal integration
  • Zoho Books: Cloud-based accounting with automated GST return generation and filing
  • ClearTax: Dedicated GST compliance platform with ITC reconciliation and e-invoicing
  • Busy Accounting: Popular with SMEs for invoice management and GST filing
  • GST Offline Tool: Free utility from GSTN for offline invoice entry and JSON upload to the portal

Conclusion

GST return filing is an ongoing compliance responsibility that requires disciplined monthly effort. The key steps are: organizing your sales and purchase invoice data, filing GSTR-1 for outward supplies by the 11th, reconciling input tax credit using GSTR-2B, filing GSTR-3B with tax payment by the 20th, and filing the annual return GSTR-9 by December 31. Late filing attracts daily late fees and 18 percent interest on unpaid tax, so maintaining a strict compliance calendar is essential.

The best approach is to use reliable accounting software, reconcile GSTR-2B with your books every month, and engage a qualified GST practitioner or Chartered Accountant for complex transactions involving exports, reverse charge, and multi-state operations. Regular reconciliation prevents year-end surprises and ensures your GST compliance remains clean for audits and assessments.

If you need professional assistance with GST return filing, ITC reconciliation, or annual return preparation, our team at IncorpX can handle your GST compliance end to end.

Frequently Asked Questions

What are the different types of GST returns that a business needs to file?
The main GST returns are: GSTR-1 for reporting outward supplies (sales), GSTR-3B for monthly summary return and tax payment, GSTR-9 for annual return, GSTR-4 for composition scheme dealers (annually), GSTR-5 for non-resident taxable persons, GSTR-6 for input service distributors, and GSTR-7 for TDS deductors under GST. Most regular businesses need to file only GSTR-1 and GSTR-3B on a monthly or quarterly basis, plus GSTR-9 annually.
What is GSTR-1 and when should it be filed?
GSTR-1 is the return for reporting all outward supplies (sales) made during a month or quarter. It contains invoice level details of all B2B (business to business) supplies, aggregate details of B2C (business to consumer) supplies, credit and debit notes, export invoices, and nil-rated or exempt supplies. Monthly filers must file GSTR-1 by the 11th of the following month. Quarterly filers under the QRMP scheme (businesses with turnover up to 5 crore rupees) must file by the 13th of the month following the quarter.
What is GSTR-3B and when is the due date?
GSTR-3B is a self-declared monthly summary return where the taxpayer reports total output tax liability, input tax credit claimed, and pays the net tax. Unlike GSTR-1 which has invoice level details, GSTR-3B contains only summarized figures. For monthly filers, GSTR-3B is due by the 20th of the following month. For quarterly filers under the QRMP scheme, the due date is the 22nd or 24th of the month following the quarter depending on the state of registration.
What is GSTR-9 and who needs to file it?
GSTR-9 is the annual GST return that consolidates all monthly or quarterly returns filed during a financial year. It must be filed by every registered taxpayer except those under the composition scheme, casual taxable persons, input service distributors, non-resident taxable persons, and persons paying TDS under GST. GSTR-9 is due by December 31 of the following financial year. Taxpayers with annual turnover up to 2 crore rupees are exempt from filing GSTR-9 as per recent simplification measures.
What is the QRMP scheme in GST?
The QRMP (Quarterly Return Monthly Payment) scheme allows small taxpayers with aggregate turnover up to 5 crore rupees in the previous financial year to file GSTR-1 and GSTR-3B on a quarterly basis instead of monthly. However, they must still pay GST on a monthly basis by the 25th of the following month using the PMT-06 challan. The quarterly return due dates are the 13th (GSTR-1) and 22nd/24th (GSTR-3B) of the month following the quarter. Under QRMP, taxpayers can use the Invoice Furnishing Facility (IFF) to upload B2B invoices in the first two months of the quarter so that their recipients can claim ITC without waiting for the quarterly GSTR-1.
How do I file GSTR-1 on the GST portal step by step?
To file GSTR-1: Log into gst.gov.in and go to Returns Dashboard. Select the return period and click Prepare Online for GSTR-1. Add invoices under the appropriate sections: B2B Invoices (enter GSTIN, invoice number, date, value, and tax), B2C invoices (enter aggregate value by rate), Credit/Debit Notes, Export Invoices, and Nil Rated Supplies. Alternatively, use the Offline Tool to upload invoices in JSON format. After entering all data, click Generate Summary and review. If everything is correct, click Submit, then File GSTR-1 using your DSC or EVC.
How do I file GSTR-3B on the GST portal step by step?
To file GSTR-3B: Log into gst.gov.in, go to Returns Dashboard, and select the GSTR-3B period. The system auto-populates some values from your GSTR-1 filing. In Table 3.1, enter outward supply details (taxable, zero-rated, nil-rated, and exempt). In Table 4, enter eligible input tax credit details. In Table 5, enter exempt, non-GST, and nil-rated inward supplies. In Table 6, review the tax computation showing output tax minus ITC and net payable. If there is a tax liability, create a challan and pay via net banking, NEFT, or credit ledger. After payment, file GSTR-3B using DSC or EVC.
What is input tax credit (ITC) in GST and how does it work?
Input Tax Credit (ITC) is the GST paid on purchases (inputs, input services, and capital goods) that can be offset against the GST collected on sales (output tax). For example, if you collect 18,000 rupees as GST on your sales and you paid 10,000 rupees as GST on your purchases, you only need to deposit the net amount of 8,000 rupees to the government. ITC is available only for purchases used in the course of business, received from GST-registered suppliers who have filed their GSTR-1, and reflected in your GSTR-2B auto-populated statement. ITC is not available for personal use items, blocked credits listed in Section 17(5), and purchases from unregistered dealers (with some exceptions).
What is GSTR-2B and how is it used for ITC reconciliation?
GSTR-2B is an auto-generated, static statement available on the GST portal for every registered taxpayer. It is generated on the 14th of every month based on the GSTR-1 returns filed by your suppliers. GSTR-2B shows all the ITC that is available to you, all the ITC that needs to be reversed, and invoices where ITC is not available. You should reconcile your purchase records with GSTR-2B before filing GSTR-3B to ensure you only claim ITC that is reflected in the system. Claiming ITC for invoices not in GSTR-2B can result in notices, interest, and penalties during annual reconciliation or GST audit.
What happens if I file GST returns late?
Late filing of GST returns attracts both late fees and interest. For GSTR-1 and GSTR-3B, the late fee is 50 rupees per day (25 CGST + 25 SGST) for regular returns and 20 rupees per day for nil returns, subject to maximum caps. For GSTR-3B, the maximum late fee is capped at 5,000 rupees for turnover up to 1.5 crore rupees, 10,000 rupees for turnover between 1.5 and 5 crore rupees, and 10,000 rupees for turnover above 5 crore rupees per return period. Additionally, interest at 18 percent per annum is charged on the net tax liability from the due date until the date of payment.
What is the GST late fee for GSTR-9 annual return?
The late fee for GSTR-9 is 200 rupees per day (100 CGST + 100 SGST) subject to a maximum of 0.50 percent of turnover in the state or 0.25 percent of turnover as CGST and 0.25 percent as SGST. For example, if your annual turnover in a state is 1 crore rupees, the maximum late fee for GSTR-9 would be 50,000 rupees (25,000 CGST + 25,000 SGST). Given these steep penalties, it is critical to file GSTR-9 well before the December 31 deadline.
What is the interest rate on late payment of GST?
The interest rates on late GST payment are: 18 percent per annum on the tax amount paid after the due date (on net tax liability after adjusting ITC), and 24 percent per annum on excess ITC wrongly claimed and utilized or tax collected but not deposited with the government. Interest is calculated from the day following the due date until the date of actual payment. Interest is charged on the net cash tax liability, not on the gross tax liability. This was clarified through an amendment effective from September 2020.
Can I revise or amend a GST return after filing?
GST returns cannot be revised or amended after filing. However, you can make corrections through subsequent returns. For GSTR-1, you can amend invoice details in the Amendment Tables (9A, 9B, 9C) of the next month's GSTR-1. For GSTR-3B, any adjustment in outward tax liability or ITC can be made in the next period's GSTR-3B by reporting the differential amount. Any errors in GSTR-9 cannot be corrected once filed, so review the annual return thoroughly before submission. Always file returns carefully the first time to avoid the complexity of amendments.
What is the composition scheme in GST and how does return filing differ?
The Composition Scheme under Section 10 of the CGST Act allows small businesses with turnover up to 1.5 crore rupees (75 lakh rupees for special category states) to pay GST at a flat rate of 1 percent (for manufacturers), 5 percent (for restaurants), or 6 percent (for service providers with turnover up to 50 lakh rupees). Composition dealers file a single annual return in GSTR-4 instead of monthly GSTR-1 and GSTR-3B. They must pay tax quarterly using CMP-08 challan by the 18th of the month following each quarter. They cannot issue tax invoices, cannot charge GST from customers, and cannot claim input tax credit.
What is the Invoice Furnishing Facility (IFF) under QRMP?
The Invoice Furnishing Facility (IFF) is available to taxpayers enrolled in the QRMP scheme. It allows quarterly filers to upload their B2B invoices for the first and second months of each quarter so that their business customers can see these invoices in their GSTR-2B and claim input tax credit without waiting for the quarterly GSTR-1. IFF invoices are uploaded by the 13th of the following month. The total value of invoices uploaded through IFF in the first two months cannot exceed 50 lakh rupees. The remaining invoices are reported in the quarterly GSTR-1 filed after the quarter ends.
How do I reconcile GSTR-1 with GSTR-3B?
Reconciling GSTR-1 with GSTR-3B means ensuring that the total taxable value and tax reported in GSTR-1 (invoice level details) matches the summary figures declared in GSTR-3B. Common reasons for mismatches include: missed invoices in GSTR-1, incorrect tax rate applied, advances received but not adjusted, credit or debit notes not properly recorded, and rounding differences. Download both GSTR-1 and GSTR-3B for each month, compare the totals for each tax head (CGST, SGST, IGST, Cess), and identify the variations. Any consistent mismatches will be flagged in GSTR-9 during annual reconciliation and may attract departmental scrutiny.
What records must I maintain for GST return filing?
Under GST law, every registered person must maintain the following records for a minimum of 72 months (6 years) from the due date of filing the annual return: Sales and purchase invoices with sequential numbering, Credit and debit notes, Input tax credit register, Stock register with quantity and value details, Accounts of advances received and adjusted, GST payment challans and bank statements, Import and export documentation, HSN or SAC wise summary of goods and services, E-way bills for goods transportation, and Job work registers if applicable. Digital records are acceptable, and cloud-based accounting software is recommended for easy retrieval during audits.
What is an E-way bill and how does it relate to GST returns?
An E-way bill is an electronic document required for the movement of goods worth more than 50,000 rupees. It is generated on the E-way Bill Portal (ewaybillgst.gov.in) and contains details of the consignor, consignee, transporter, goods description, value, and GST details. While E-way bills are not directly part of GST returns, the invoice details in E-way bills must match the invoices reported in GSTR-1. Any discrepancy between E-way bill data and GSTR-1 data can trigger departmental notices. Additionally, E-way bill data is used by the GST authorities for cross-verification and anti-evasion analysis.
What is the HSN code and why is it important in GST return filing?
HSN (Harmonized System of Nomenclature) codes classify goods systematically for GST purposes. HSN codes are mandatory in GST returns: taxpayers with turnover above 5 crore rupees must mention 6-digit HSN codes, and those with turnover up to 5 crore rupees must mention 4-digit HSN codes in their invoices and GSTR-1. For services, SAC (Services Accounting Code) numbers are used instead. Correct HSN/SAC codes ensure the right GST rate is applied and prevent misclassification issues during assessment. The HSN summary is also required in Table 12 of GSTR-1 and in GSTR-9 annual return.
How do I claim a GST refund?
GST refunds can be claimed in specific scenarios: refund of excess tax paid, refund on exports (either duty paid or under bond/LUT), refund of accumulated ITC due to inverted duty structure (input tax rate higher than output tax rate), refund on supplies to SEZ units, and refund of advance tax where supply did not materialize. To claim a refund, file Form RFD-01 on the GST portal within 2 years from the relevant date, attach supporting documents including invoices and bank statements, and submit. The refund is processed within 60 days. For exports, you can either pay IGST and claim a refund or export under bond/LUT with accumulated ITC refund.
What is GSTR-9C and who needs to file it?
GSTR-9C is the reconciliation statement that was previously required to be certified by a Chartered Accountant for taxpayers with turnover above 5 crore rupees. From FY 2020-21 onwards, GSTR-9C is a self-certified reconciliation statement that the taxpayer can file without CA certification. It requires reconciliation of the figures reported in GSTR-9 with the audited financial statements. GSTR-9C is mandatory for taxpayers with turnover exceeding 5 crore rupees and must be filed along with GSTR-9 by December 31 of the following financial year.
What happens if there is a mismatch between my books and GST returns?
Mismatches between books of accounts and GST returns can arise from timing differences, missed invoices, incorrect classifications, or ITC reversals. If the GST department identifies a mismatch during scrutiny or audit, they issue a notice under Section 61 asking for an explanation. If the discrepancy leads to short payment of tax, a demand notice is issued under Section 73 (for non-fraud cases with 12 months limitation) or Section 74 (for fraud cases with 5 years limitation). Penalties range from 10 percent of tax due to 100 percent of tax due depending on whether fraud is involved. Regular monthly reconciliation prevents such issues.
Can I file GST returns using accounting software?
Yes, most modern accounting software packages like Tally Prime, Zoho Books, ClearTax, Busy Accounting, and others support direct GST return filing. These tools allow you to record sales and purchase invoices, automatically calculate GST, generate GSTR-1 and GSTR-3B data in the required format, and push the data directly to the GST portal through API integration. Some software also provides GSTR-2B reconciliation, ITC matching, and annual return preparation features. Using accounting software significantly reduces manual errors and saves time compared to filing on the GST portal directly.
What is the nil return in GST and how do I file it?
A nil GST return must be filed when you have no sales, no purchases, and no tax liability during a return period. Even if your business had zero activity, filing nil returns is mandatory to maintain your active GST registration status. To file a nil GSTR-1, log into the GST portal, select GSTR-1, and click on File Nil GSTR-1. For nil GSTR-3B, go to the GSTR-3B dashboard and click File Nil Return. You can also file nil returns through SMS by sending the prescribed format to the GST portal's registered mobile number. Late fee for nil returns is reduced to 20 rupees per day (10 CGST + 10 SGST).
What is the difference between CGST, SGST, IGST, and Cess?
CGST (Central GST) and SGST (State GST) are levied on intra-state supplies (supplies within the same state), with each going to the central and state government respectively. IGST (Integrated GST) is levied on inter-state supplies (supplies between different states) and on imports, and goes to the central government which then settles the state's share. GST Cess is an additional tax levied on specific goods like luxury cars, tobacco, and aerated drinks over and above the applicable GST rate. All four components must be correctly reported in GSTR-1 and GSTR-3B based on the place of supply rules.
How do I determine if a supply is intra-state or inter-state for GST?
The determination is based on the place of supply rules defined in Sections 10 to 13 of the IGST Act. If the location of the supplier and the place of supply are in the same state, it is an intra-state supply attracting CGST + SGST. If they are in different states, it is an inter-state supply attracting IGST. For goods, the place of supply is generally where the goods are delivered. For services, it depends on the nature of the service: for most services it is the location of the recipient, for immovable property related services it is the location of the property, and for event services it is the location of the event.
What is reverse charge mechanism (RCM) in GST?
Under the Reverse Charge Mechanism (RCM), the recipient of goods or services pays the GST instead of the supplier. RCM applies in two scenarios: Section 9(3) covers specified categories of supplies notified by the government (such as legal services from advocates, goods transport by GTA, and services by directors to companies), and Section 9(4) covers supplies received from unregistered persons by registered persons for certain specified categories. The recipient must self-invoice, pay GST on the RCM supply, and report it separately in Table 3.1(d) of GSTR-3B. ITC on RCM payments is available in the same month if all conditions are met.
What are the consequences of not filing GST returns?
Not filing GST returns has severe consequences: Late fees accumulate daily up to the prescribed maximum, Interest at 18 percent is charged on unpaid tax, your ability to file subsequent returns is blocked (you cannot file GSTR-3B for the current month without filing the previous month's returns), you cannot generate E-way bills for goods movement, your GST registration may be cancelled suo motu by the department after 6 months of continuous non-filing, and you lose the ability to claim input tax credit for the non-filed periods. Cancellation of GST registration requires filing all pending returns with late fees before reactivation.
How do I file GST returns for exports?
Exporters have two options for GST: Option 1: Export with IGST payment where you pay IGST on export invoices and claim a refund through the customs automated refund system linked to shipping bills. Option 2: Export under Bond or LUT (Letter of Undertaking) where you do not pay IGST on exports and instead claim a refund of accumulated input tax credit through Form RFD-01. In GSTR-1, report export invoices separately in Table 6A with shipping bill number and port code. In GSTR-3B, report exports in Table 3.1(b) as zero-rated supplies. Most exporters prefer the LUT option as it avoids cash flow blockage.
What is the Electronic Credit Ledger and Electronic Cash Ledger in GST?
The Electronic Credit Ledger maintains a record of all input tax credit available to the taxpayer, credited based on GSTR-3B filings. This credit can be used to offset output tax liability. The Electronic Cash Ledger maintains a record of all cash deposits made by the taxpayer through challans via net banking, NEFT, RTGS, or over the counter. When paying GST through GSTR-3B, the system first adjusts credit from the Electronic Credit Ledger against the output liability, and any remaining tax must be paid from the Electronic Cash Ledger. You can check both ledger balances on the GST portal under Electronic Ledgers section.
How do I handle credit notes and debit notes in GST returns?
Credit notes are issued when there is a reduction in taxable value after the original invoice (due to returns, discounts, or corrections). Debit notes are issued when there is an increase in taxable value. Credit notes must be reported in Table 9B of GSTR-1 and they reduce the output tax liability in GSTR-3B. Debit notes are reported in Table 9B of GSTR-1 and increase the output tax liability. Credit notes for a financial year must be declared in the GST return filed by November 30 of the following financial year or the date of filing the annual return, whichever is earlier. Any credit note issued after this deadline cannot reduce the tax liability.
What is the difference between B2B and B2C invoices in GSTR-1?
In GSTR-1, B2B (Business to Business) invoices are supplies made to other GST-registered businesses. These must be reported at invoice level with the recipient's GSTIN, invoice number, date, value, and tax amount. This data populates the recipient's GSTR-2B for ITC claims. B2C (Business to Consumer) invoices are supplies made to unregistered persons. B2C supplies are reported in aggregate: B2C Large (inter-state B2C invoices exceeding 2.5 lakh rupees) require invoice level reporting, while B2C Small (all other B2C sales) are reported as consolidated state-wise summaries.
How do I pay GST online through the GST portal?
To pay GST online: Log into gst.gov.in, go to Services, then Payments, and click Create Challan. Enter the amount to be paid for each tax head (CGST, SGST, IGST, Cess). Select the payment mode: Net Banking (available through authorized banks), NEFT/RTGS (generates a mandate form for bank transfer), Over the Counter (cash/cheque/DD at authorized bank branches for amounts up to 10,000 rupees per challan), or Credit/Debit Card where available. After payment, the amount is credited to your Electronic Cash Ledger. You then use GSTR-3B to offset this cash ledger against your tax liability along with any available credit ledger balance.
What is GST TDS and who needs to deduct it?
GST TDS (Tax Deducted at Source) under Section 51 of the CGST Act applies to specified categories of recipients including government departments, local authorities, government agencies, and entities notified by the government. When the contract value exceeds 2.5 lakh rupees, the deductor must deduct GST TDS at 2 percent (1 percent CGST + 1 percent SGST for intra-state, or 2 percent IGST for inter-state) from the payment made to the supplier. The deductor files GSTR-7 by the 10th of the following month. The deductee (supplier) can see the TDS credit in their Electronic Cash Ledger and claim it while filing GSTR-3B.
How do I cancel or surrender my GST registration?
To cancel GST registration voluntarily, log into the GST portal and file Form REG-16 under the Cancellation of Registration option. Enter the reason for cancellation, the date from which you wish to cancel, details of closing stock and applicable tax on it, and any other relevant information. You must file a final return in GSTR-10 within 3 months of the cancellation date or the date of cancellation order, whichever is later. All pending returns including GSTR-1 and GSTR-3B must be filed with late fees before cancellation is approved. Pay any tax due on closing stock as this stock will not be eligible for ITC claim by any future registrant.
What is the role of a GST practitioner in return filing?
A GST Practitioner is a qualified professional authorized to prepare and file GST returns on behalf of registered taxpayers. GST Practitioners can prepare and file GSTR-1, GSTR-3B, GSTR-9, and other returns, file applications for registration, amendment, and cancellation, and represent taxpayers before GST authorities. To become a GST Practitioner, one must be a CA, CS, CMA, Advocate, or a graduate with five years of relevant experience, and pass the GST Practitioner exam. Engaging a GST Practitioner is recommended for businesses that lack in-house GST expertise, especially for complex transactions involving exports, RCM, and multi-state operations.
How do I file a GST return if my business has multiple GSTINs?
If your business operates in multiple states, you will have a separate GSTIN for each state. Each GSTIN requires independent return filing. This means you must file separate GSTR-1, GSTR-3B, and GSTR-9 for each state registration. Inter-branch transfers between your own GSTINs in different states are treated as deemed supplies and attract IGST. Use accounting software that supports multi-GSTIN management to consolidate data and ensure consistency across all state returns. Many businesses also use a centralized compliance team or outsource multi-state GST filing to a professional firm for accuracy.
What changes were introduced in GST return filing for 2025 and 2026?
Key recent changes include: Mandatory GSTR-2B based ITC matching where ITC claims exceeding 5 percent of the eligible ITC in GSTR-2B are restricted, HSN code reporting made mandatory at 6-digit level for taxpayers with turnover above 5 crore rupees, Table 3.2 of GSTR-3B requires detailed breakup of inter-state supplies to unregistered and composition dealers, GSTR-1 Table 14 and 15 for reporting supplies to e-commerce operators, GSTR-9C self-certification replaces mandatory CA certification, and the introduction of automated return scrutiny through the GST portal's ASMT-10 notices for discrepancy resolution.
How is ITC reversed in GST and when is reversal required?
ITC reversal is required in several situations: Rule 42 requires proportional reversal of ITC used partly for taxable and partly for exempt supplies. Rule 43 applies similarly for capital goods used partly for taxable and partly for exempt supplies. Section 17(5) lists blocked credits where ITC is not available at all (motor vehicles, food and beverages for employees, personal use items, etc.). Section 16(2) requires reversal if payment is not made to the supplier within 180 days. ITC also requires reversal when goods are destroyed, written off, or given as free samples. ITC reversals are reported in Table 4(B) of GSTR-3B.
What is the time limit for claiming input tax credit in GST?
The time limit for claiming ITC for any invoice or debit note is the earlier of: the 30th of November following the end of the financial year to which the invoice belongs, or the date of filing the annual return (GSTR-9) for that financial year. For example, ITC for invoices dated in FY 2025-26 must be claimed by November 30, 2026 or the date of filing GSTR-9 for FY 2025-26, whichever is earlier. After this deadline, ITC for those invoices is permanently lost. This makes monthly reconciliation of GSTR-2B critically important to ensure no eligible credit is missed.
How does GST apply to e-commerce sellers and operators?
E-commerce operators like Amazon, Flipkart, and Swiggy must collect TCS (Tax Collected at Source) at 1 percent (0.5 percent CGST + 0.5 percent SGST/IGST) on the net value of taxable supplies made through their platform. The operator files GSTR-8 by the 10th of the following month. Sellers on e-commerce platforms must have mandatory GST registration regardless of their turnover (Section 24(ix)). They file regular GSTR-1 and GSTR-3B. The TCS collected by the operator is reflected in the seller's Electronic Cash Ledger and can be used for tax payment. E-commerce sellers cannot opt for the composition scheme.
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Dhanush Prabha is the Chief Technology Officer and Chief Marketing Officer at IncorpX, where he leads product engineering, platform architecture, and data-driven growth strategy. With over half a decade of experience in full-stack development, scalable systems design, and performance marketing, he oversees the technical infrastructure and digital acquisition channels that power IncorpX. Dhanush specializes in building high-performance web applications, SEO and AEO-optimized content frameworks, marketing automation pipelines, and conversion-focused user experiences. He has architected and deployed multiple SaaS platforms, API-first applications, and enterprise-grade systems from the ground up. His writing spans technology, business registration, startup strategy, and digital transformation - offering clear, research-backed insights drawn from hands-on engineering and growth leadership. He is passionate about helping founders and professionals make informed decisions through practical, real-world content.