How to File GST Return

Filing Goods and Services Tax (GST) returns is a mandatory compliance requirement for businesses registered under the GST regime in India. Whether you’re a small trader, a medium-sized manufacturer, or a large e-commerce operator, timely and accurate filing of GST returns ensures legal compliance, avoids penalties, and enables seamless input tax credit (ITC) claims. The GST system was designed to simplify indirect taxation by replacing multiple state and central taxes with a unified structure. However, its complexity lies in the variety of return forms, due dates, and documentation requirements that vary based on business type and turnover.

This comprehensive guide walks you through the entire process of filing GST returns—from understanding the different return types to submitting them correctly on the GST portal. We cover practical step-by-step instructions, industry best practices, essential tools, real-world examples, and answers to frequently asked questions. By the end of this tutorial, you’ll have the knowledge and confidence to file your GST returns accurately and on time, every time.

Step-by-Step Guide

Filing a GST return involves multiple stages, each requiring attention to detail. The process differs slightly depending on the type of taxpayer—regular taxpayer, composition dealer, non-resident taxable person, or input service distributor. This section focuses on the most common scenario: a regular taxpayer filing GSTR-1, GSTR-3B, and GSTR-9.

Step 1: Determine Your Return Filing Frequency

Before you begin filing, identify your return filing frequency. Most regular taxpayers file monthly returns, while small businesses with an annual turnover up to ₹5 crore can opt for quarterly filing under the QRMP (Quarterly Return Monthly Payment) scheme. Composition dealers file GSTR-4 quarterly, and non-resident taxable persons file GSTR-5 monthly.

To confirm your filing frequency, log in to the GST portal (www.gst.gov.in) and check your registration details under “Services > Registration > Amendment of Registration Non-Core Fields.” Your return filing frequency will be listed under “Return Filing Frequency.”

Step 2: Gather Required Documents and Data

Accurate filing begins with accurate data. Collect the following documents before you start:

• Invoice register (outward and inward supplies)
• Bank statements and payment records
• Details of credit notes and debit notes issued/received
• Details of ITC claimed from GSTR-2A/2B
• Previous month’s GSTR-3B summary
• Details of exempt, nil-rated, and non-GST supplies
• HSN/SAC codes for goods and services

Ensure your accounting software or ledger system is updated and reconciled with your sales and purchase records. Any mismatch between your books and GST portal data can lead to discrepancies during reconciliation.

Step 3: File GSTR-1 (Outward Supplies)

GSTR-1 is the monthly or quarterly return detailing all outward supplies made by a taxpayer. It includes sales invoices, credit notes, debit notes, and details of exports and zero-rated supplies.

To file GSTR-1:

1. Log in to the GST portal using your credentials.
2. Navigate to Services > Returns > Returns Dashboard.
3. Select the appropriate financial year and return filing period.
4. Click on Prepare Online under GSTR-1.
5. Enter details under the following sections:

• Table 4: B2B Supplies – Details of invoices issued to registered taxpayers. Include invoice number, date, recipient GSTIN, taxable value, rate, and tax amount.
• Table 5: B2C Large – Invoices exceeding ₹2.5 lakh to unregistered persons. State-wise summary required.
• Table 6: B2C Small – Invoices up to ₹2.5 lakh. Summary by rate and state.
• Table 7: Exports – Details of goods and services exported with shipping bill or bill of export number.
• Table 8: Credit/Debit Notes – Adjustments made to previous invoices.
• Table 9: Nil-rated, Exempt, Non-GST Supplies – Summary of supplies not attracting GST.
• Table 10: HSN Summary – Aggregate value and tax for goods based on HSN codes (mandatory for turnover > ₹5 crore).
• Table 11: Service Accounting Code (SAC) Summary – For services (mandatory for turnover > ₹5 crore).

After entering all data, validate the form using the Validate button. Correct any errors or warnings. Once validated, proceed to Preview and then Submit. You will receive an acknowledgment number (ARN) upon successful submission.

Important: GSTR-1 must be filed before the 11th of the next month for monthly filers, or the 13th of the month following the quarter for quarterly filers.

Step 4: Review GSTR-2A and GSTR-2B

GSTR-2A is an auto-drafted, read-only statement showing all inward supplies based on GSTR-1 filings by your suppliers. GSTR-2B is a static, monthly ITC statement generated on the 12th of each month, reflecting eligible input tax credit.

Use these statements to reconcile your purchase records with supplier filings:

• Compare your purchase register with GSTR-2A to identify missing invoices or mismatches.
• Verify that all invoices with correct GSTINs and tax amounts appear in GSTR-2B.
• Do not claim ITC on invoices not reflected in GSTR-2B. Only ITC reflected in GSTR-2B is eligible for claiming.
• Report discrepancies to your suppliers for corrections in their GSTR-1.

Reconciliation should be completed before filing GSTR-3B to avoid claiming ineligible credit or missing eligible credit.

Step 5: File GSTR-3B (Summary Return)

GSTR-3B is a simplified monthly or quarterly summary return used to declare output tax liability, ITC claimed, and tax payable. It is filed even if there are no transactions during the period (nil return).

To file GSTR-3B:

1. Log in to the GST portal and go to Services > Returns > Returns Dashboard.
2. Select the financial year and return period.
3. Click on Prepare Online under GSTR-3B.
4. Fill in the following sections:

• Table 3: Details of Outward Supplies and Inward Supplies (liable to reverse charge) – Summarize taxable value and tax liability from GSTR-1. Include B2B, B2C, exports, and nil-rated supplies.
• Table 4: Eligible ITC – Claim ITC from GSTR-2B under categories: inward supplies (other than reverse charge), import of services, and ITC on capital goods.
• Table 5: ITC Reversal – Report ITC reversed due to non-payment within 180 days, exempt supplies, or non-business use.
• Table 6: Tax Payable – Calculate net tax liability: Output Tax – ITC Claimed + Reverse Charge Tax + Interest + Penalty.
• Table 7: Payment of Tax – Use the Electronic Cash Ledger or Electronic Credit Ledger to pay liability. Select payment mode and enter challan details.

After entering all values, validate the form. Cross-check your calculations with GSTR-1 and GSTR-2B data. Once verified, submit the return. You will receive an ARN. Pay any outstanding tax using the challan generated before the due date (20th of the next month for monthly filers).

Step 6: File GSTR-9 (Annual Return)

GSTR-9 is the annual return that consolidates all monthly/quarterly returns filed during the financial year. It is mandatory for all regular taxpayers (except composition dealers, input service distributors, non-resident taxable persons, and casual taxable persons).

To file GSTR-9:

1. Log in to the GST portal and navigate to Services > Returns > Annual Return.
2. Select the financial year and click Prepare Online.
3. The system auto-populates data from your GSTR-1 and GSTR-3B filings. Review each section carefully:

• Part I: Basic Details – Confirms your GSTIN, name, and financial year.
• Part II: Sales and Purchase Details – Summarizes outward and inward supplies, reconciled with GSTR-1 and GSTR-2A.
• Part III: ITC Details – Summarizes ITC claimed, reversed, and ineligible credit.
• Part IV: Tax Paid – Shows total tax paid via cash and credit ledgers.
• Part V: Other Information – Includes HSN summary, advances received, and adjustments.
• Part VI: Late Fees Payable – Auto-calculated if any return was filed late.

Make necessary corrections if auto-populated data is incorrect. You can manually override fields if supported. After validation, preview, and submit. Pay any late fee due before final submission. The due date for GSTR-9 is December 31 of the following financial year.

Step 7: File GSTR-9C (Audit Reconciliation Statement)

Businesses with an annual turnover exceeding ₹5 crore must get their accounts audited by a Chartered Accountant and file GSTR-9C, a reconciliation statement between financial statements and GST returns.

To file GSTR-9C:

1. Obtain a certified reconciliation statement from a practicing Chartered Accountant.
2. Log in to the GST portal and go to Services > Returns > Annual Return.
3. Click on Prepare Online for GSTR-9C.
4. Upload the signed and certified GSTR-9C form in PDF format.
5. Submit the form after verification.

Ensure the CA’s report matches your GSTR-9 data. Discrepancies may trigger scrutiny or audit notices from tax authorities.

Best Practices

Filing GST returns accurately and on time is not just a compliance requirement—it’s a strategic business practice. Here are proven best practices to streamline your GST return filing process and minimize risks.

Maintain Real-Time Record Keeping

Delaying bookkeeping until the end of the month is a common mistake. Use accounting software that integrates with the GST portal to auto-generate invoice data. Regular reconciliation (daily or weekly) prevents last-minute errors and ensures data consistency across systems.

Use GST-Compliant Invoicing

Every invoice must include mandatory fields: GSTIN of buyer and seller, invoice number and date, HSN/SAC code, taxable value, tax rate, and tax amount. Non-compliant invoices may be rejected by recipients, leading to ITC denial. Use templates pre-approved by GSTN to ensure compliance.

Reconcile GSTR-2B Monthly

Many taxpayers overlook GSTR-2B and rely on GSTR-2A, which is dynamic and subject to change. GSTR-2B is the authoritative source for ITC eligibility. Always use GSTR-2B data to claim credit. Discrepancies should be flagged and resolved with suppliers within 15 days of receipt.

File Returns Early

Don’t wait until the last day. Filing early gives you time to address technical glitches, system errors, or supplier delays. It also allows you to plan your tax payments and avoid interest on late payments. Set internal deadlines 3–5 days before the official due date.

Keep Backup of All Filings

Download and save PDF copies of all filed returns (GSTR-1, GSTR-3B, GSTR-9, GSTR-9C) along with ARNs. Store them securely for at least six years. In case of disputes or audits, these documents serve as legal proof of compliance.

Train Your Finance Team

GST rules evolve frequently. Conduct quarterly training sessions for your accounts team on changes in return formats, due dates, and ITC eligibility. Stay updated through official GSTN circulars and notifications.

Use Reconciliation Tools

Manual reconciliation of thousands of invoices is error-prone. Use GST reconciliation tools like ClearTax, Zoho Books, or Tally.ERP 9 that offer auto-matching of GSTR-1 and GSTR-2A/2B data. These tools highlight mismatches and suggest corrections.

Monitor Late Fee and Interest

Late filing of GSTR-1 or GSTR-3B attracts penalties. For GSTR-3B, late fees are ₹50 per day (₹25 under CGST and ₹25 under SGST) up to ₹5,000. Interest at 18% per annum is charged on delayed tax payments. Set calendar reminders to avoid these costs.

Plan for Nil Returns

Even if you have no sales or purchases in a month, you must file a nil return. Failure to file nil returns may result in your GSTIN being marked as non-compliant, affecting your ability to issue invoices or claim ITC.

Tools and Resources

Leveraging the right tools and resources can significantly reduce the time and effort required to file GST returns accurately. Below are essential tools and official resources recommended for businesses of all sizes.

Official GST Portal

The GST portal (www.gst.gov.in) is the primary platform for all return filings, ITC reconciliation, and tax payments. It offers downloadable forms, FAQs, and video tutorials. Always use the official portal—never third-party sites claiming to file on your behalf without authorization.

Accounting Software Integrations

Modern accounting platforms offer seamless GST compliance features:

• Tally.ERP 9 – Auto-generates GSTR-1 and GSTR-3B from ledger entries. Supports HSN/SAC mapping and e-invoicing.
• Zoho Books – Integrates with GSTN for e-invoicing and return filing. Ideal for SMEs.
• ClearTax GST Software – Offers reconciliation, audit trails, and real-time ITC tracking.
• Khatabook – Simplified invoicing and return filing for small traders and retailers.

Choose software that supports e-invoicing (if your turnover exceeds ₹5 crore) and provides auto-fill features for GSTR-1 and GSTR-3B.

GSTN’s Official Resources

The GST Network provides free, authoritative resources:

• GST Helpdesk – Accessible via the portal for technical queries.
• FAQ Section – Covers return filing, ITC, e-invoicing, and more.
• Video Tutorials – Step-by-step guides on filing GSTR-1, GSTR-3B, and GSTR-9.
• Notifications and Circulars – Updated regularly on changes to filing procedures.

Reconciliation Tools

Third-party reconciliation tools help identify mismatches and streamline ITC claims:

• GSTN Reconciliation Tool – Free tool on the GST portal to compare GSTR-1 and GSTR-2A.
• RightTax – AI-powered reconciliation engine with alerts for missing invoices.
• Enterslice GST Compliance Suite – End-to-end compliance tracking including due date alerts.

Mobile Apps

For on-the-go access:

• GSTN Mobile App – View ARNs, due dates, and payment status.
• ClearTax GST App – File returns and track ITC from your smartphone.

Professional Assistance

For complex businesses—especially those with multiple GSTINs, interstate operations, or high-value exports—consulting a GST practitioner or CA can prevent costly errors. Many firms offer annual compliance packages that include return filing, reconciliation, and audit support.

Real Examples

Understanding GST return filing becomes easier with real-world scenarios. Below are three examples illustrating how different types of businesses file their returns.

Example 1: Small Retailer (Turnover < ₹5 Crore, Quarterly Filer)

Mr. Rajesh runs a small electronics retail store in Pune with a quarterly turnover of ₹3.2 crore. He files under the QRMP scheme.

• April–June 2024: He issues 87 B2B invoices and 215 B2C invoices (all below ₹2.5 lakh). He files GSTR-1 by July 13, summarizing B2B details in Table 4 and B2C in Table 6.
• GSTR-3B: He claims ₹1.2 lakh ITC from GSTR-2B, reports ₹2.8 lakh output tax, and pays ₹1.6 lakh net tax via cash ledger. He files GSTR-3B by July 20.
• Annual Return: In December 2024, he files GSTR-9, reconciling all quarterly returns. No audit is required as turnover is below ₹5 crore.

Result: Timely filing avoids penalties, and his ITC claims are fully accepted.

Example 2: E-commerce Seller (Turnover > ₹5 Crore, Monthly Filer)

Shree Enterprises is an e-commerce seller on Amazon, with monthly sales of ₹8 crore. They are required to file monthly returns and e-invoice their supplies.

• May 2024: They issue 1,450 e-invoices via the Invoice Registration Portal (IRP). GSTR-1 is filed by June 11, including HSN summary (Table 10) and details of supplies to e-commerce operators (Table 4A).
• GSTR-3B: They claim ₹92 lakh ITC, report ₹1.1 crore output tax, and pay ₹18 lakh net tax. They reconcile GSTR-2B daily using ClearTax software.
• GSTR-9 and GSTR-9C: In December 2024, they file GSTR-9 and get their books audited. The CA identifies a ₹4.2 lakh ITC mismatch due to delayed supplier filings. They adjust it in the annual return and pay interest.

Result: Automation and professional audit help maintain compliance despite high transaction volume.

Example 3: Export-Oriented Manufacturer

Global Textiles Ltd. exports 90% of its goods and has a turnover of ₹12 crore. They file monthly returns and claim refunds for zero-rated supplies.

• March 2024: They issue 32 export invoices with shipping bill numbers under Table 6A of GSTR-1. They file GSTR-1 by April 11.
• GSTR-3B: They declare zero tax on exports and claim ITC on inputs used for export production. They file a refund application (RFD-01) on the GST portal for ₹5.4 lakh input tax credit.
• Annual Return: In GSTR-9, they reconcile all export invoices with customs data. The refund is processed by August 2024.

Result: Proper documentation of exports and timely refund applications ensure liquidity and compliance.

FAQs

What happens if I miss the GST return filing deadline?

If you file late, you’ll incur a late fee of ₹50 per day (₹25 under CGST and ₹25 under SGST), capped at ₹5,000. Additionally, interest at 18% per annum is charged on outstanding tax liability. Persistent non-filing may lead to suspension of your GSTIN.

Can I file a nil GST return?

Yes. Even if you have no sales, purchases, or tax liability during a tax period, you must file a nil return. Failing to do so may result in your GSTIN being flagged as non-compliant.

How do I correct a mistake in a filed GST return?

You cannot amend a filed GSTR-3B directly. Corrections must be made in subsequent returns. For GSTR-1, you can revise it in the next filing period using the amendment tables (Table 9A for B2B, Table 11A for HSN). For GSTR-9, you can file a revised return before December 31 of the next financial year.

Why is my ITC not reflecting in GSTR-2B?

Common reasons include: supplier has not filed GSTR-1, invoice details are mismatched (GSTIN, amount, tax rate), or the invoice is not uploaded on the GST portal. Contact your supplier to correct their filing or wait until the next GSTR-2B generation.

Is HSN code mandatory for all businesses?

Yes, but with thresholds. Businesses with turnover up to ₹5 crore must mention HSN code only if turnover exceeds ₹5 crore. For services, SAC code is mandatory for turnover above ₹5 crore.

Can I claim ITC on reverse charge supplies?

Yes, you can claim ITC on reverse charge supplies if they are used for business purposes and the tax has been paid. Ensure the invoice clearly mentions reverse charge and your GSTIN.

What is the difference between GSTR-2A and GSTR-2B?

GSTR-2A is a dynamic, real-time summary of inward supplies based on suppliers’ GSTR-1 filings. GSTR-2B is a static, auto-generated ITC statement on the 12th of each month, based on finalized GSTR-1 and GSTR-5 filings. Only GSTR-2B data is eligible for ITC claims.

Do I need to file GSTR-9C if my turnover is below ₹5 crore?

No. GSTR-9C is mandatory only for taxpayers with annual turnover exceeding ₹5 crore. Smaller businesses need to file only GSTR-9.

Can I file GST returns without a CA?

Yes. Any registered taxpayer can file their own returns using the GST portal. However, for complex businesses, high turnover, or audit requirements, professional assistance is recommended to avoid errors and penalties.

What documents should I keep after filing GST returns?

Keep PDF copies of all filed returns (GSTR-1, GSTR-3B, GSTR-9, GSTR-9C), ARNs, payment challans, invoice registers, bank statements, and reconciliation reports. Retain them for at least six years from the end of the financial year to which they pertain.

Conclusion

Filing GST returns is a critical component of running a compliant and efficient business in India. While the process may appear complex due to multiple forms, deadlines, and reconciliation requirements, a systematic approach transforms it from a burden into a streamlined operational task. By following the step-by-step guide outlined in this tutorial, adhering to best practices, utilizing digital tools, and learning from real examples, you can ensure accuracy, avoid penalties, and maximize your input tax credit benefits.

The key to success lies in consistency—regular record keeping, monthly reconciliation, early filing, and staying updated with regulatory changes. Whether you’re a small trader or a large manufacturer, GST compliance is not optional; it’s foundational to sustainable growth. Embrace technology, invest in training, and treat GST filing as a strategic function rather than a mere formality.

With discipline and the right resources, filing GST returns becomes not just a legal obligation, but a competitive advantage—enhancing your credibility with suppliers, customers, and tax authorities alike.