GST Portal: How to File GSTR-1, GSTR-3B & GSTR-9 (Step-by-Step with Screenshots)

Understanding the Three Core GST Returns

Every GST-registered business in India must file multiple returns throughout the year. For regular taxpayers—including foreign companies operating through Indian subsidiaries—three returns form the backbone of GST compliance:

These returns are interconnected. GSTR-1 data auto-populates into your buyers' GSTR-2B (their input tax credit statement). GSTR-3B is where you actually pay your tax liability after adjusting input tax credit. GSTR-9 reconciles the entire year's GSTR-1 and GSTR-3B data into a single comprehensive document.

Getting any of these wrong—or filing them late—triggers penalties, blocks your buyers' input tax credit, and can result in your GST registration being marked for cancellation. Here is the exact process for each.

GSTR-1: Filing Outward Supply Details

What GSTR-1 Captures

GSTR-1 records every sale (outward supply) your business makes during a tax period. It includes:

• B2B invoices: Sales to other GST-registered businesses (reported invoice-by-invoice with buyer's GSTIN)
• B2C large invoices: Inter-state sales to unregistered persons exceeding INR 2.5 lakh (reported invoice-by-invoice)
• B2C small invoices: All other sales to unregistered persons (reported as state-wise summary)
• Credit/debit notes: Adjustments to previously reported invoices
• Export invoices: Sales to customers outside India
• Advances received: Advance payments received for which invoices have not yet been issued
• HSN summary: Commodity-wise summary of all outward supplies

If your company uses e-invoicing (mandatory for businesses with turnover above INR 5 crore), most B2B invoice data auto-populates into GSTR-1 from the Invoice Registration Portal (IRP). You still need to add B2C summaries and verify the auto-populated data.

Who Files Monthly vs. Quarterly

• Monthly filing: Businesses with aggregate turnover exceeding INR 5 crore in the previous financial year. Due date: 11th of the following month.
• Quarterly filing (QRMP scheme): Businesses with turnover up to INR 5 crore can opt for quarterly filing. Due date: 13th of the month following the quarter. However, they must still use the Invoice Furnishing Facility (IFF) to upload B2B invoices in the first two months of each quarter.

Most foreign subsidiaries operating in India exceed the INR 5 crore threshold and file monthly.

Step-by-Step: Filing GSTR-1 on the GST Portal

1. Log in to gst.gov.in using your GSTIN, username, and password
2. Navigate to Services > Returns > Returns Dashboard
3. Select the financial year and return filing period (month or quarter) from the dropdown
4. Click Search to load the return filing page
5. Under the GSTR-1 tile, click "Prepare Online" (for manual entry) or "Prepare Offline" (for bulk upload via JSON/Excel utility)
6. Add B2B invoices: Enter each invoice with buyer GSTIN, invoice number, date, taxable value, and GST rates. If e-invoicing is active, verify the auto-populated data instead.
7. Add B2C (Large) invoices: Enter inter-state B2C invoices above INR 2.5 lakh with place of supply, invoice details, and tax amounts
8. Add B2C (Small) summary: Enter state-wise consolidated summary of all other B2C sales with rate-wise breakup
9. Add credit/debit notes: Enter any adjustments to previously reported invoices
10. Add export invoices: Report export sales with shipping bill number, port code, and whether exports are with or without payment of IGST
11. Review HSN summary: Verify the HSN-wise breakup of your outward supplies
12. Preview the return: Click "Generate GSTR-1 Summary" to review all sections
13. File the return: Click "Submit" to freeze the data, then "File Return" using either EVC (OTP on registered mobile and email) or DSC (Digital Signature Certificate of the authorized signatory)

GSTR-1 Late Fees

In addition to late fees, interest at 18% per annum applies on any unpaid tax from the due date until payment. Late GSTR-1 filing also delays your buyers' ability to claim input tax credit on your invoices, which can damage business relationships.

GSTR-3B: Summary Return and Tax Payment

What GSTR-3B Captures

GSTR-3B is a self-declared summary return where you report:

• Table 3.1: Tax on outward supplies—total taxable value and tax collected on sales, exports, and supplies to SEZ
• Table 3.2: Inter-state supplies to unregistered persons, composition dealers, and UIN holders (auto-populated from GSTR-1 from November 2025 onwards, non-editable)
• Table 4: Eligible input tax credit (ITC)—the GST you paid on purchases that you can offset against your tax liability
• Table 5: Exempt, nil-rated, and non-GST inward supplies
• Table 6: Payment of tax—the actual tax you owe after adjusting ITC, paid using the electronic credit ledger or electronic cash ledger

GSTR-3B is where the actual tax payment happens. Your GSTR-1 reports sales details; GSTR-3B reports the summary and settles the tax.

Important 2025-2026 Changes

• Auto-population from GSTR-1: From the February 2026 tax period onwards, the GST Portal auto-populates the "Tax Liability Breakup, As Applicable" section for any interest or tax belonging to a previous period but being discharged in the current period's GSTR-3B
• Non-editable Table 3.2: From November 2025, auto-populated values in Table 3.2 from GSTR-1/1A/IFF become non-editable. You must use system-generated values only.
• Three-year filing window: From the July 2025 tax period onwards, taxpayers cannot file GSTR-3B after the expiry of three years from the due date of that period's return

Step-by-Step: Filing GSTR-3B on the GST Portal

1. Log in to gst.gov.in and navigate to Services > Returns > Returns Dashboard
2. Select the financial year and return filing period from the dropdown and click Search
3. Under the GSTR-3B tile, click "Prepare Online"
4. Table 3.1 – Outward supplies: Enter the total taxable value and tax amount for outward supplies subject to tax, zero-rated supplies, and supplies to SEZ. Verify against your GSTR-1 figures.
5. Table 3.2 – Inter-state supplies: This is now auto-populated and non-editable from November 2025 onwards. Review for accuracy.
6. Table 4 – Input Tax Credit (ITC): Enter the ITC available for the period. Cross-check with GSTR-2B (your auto-generated ITC statement). Report ITC reversed due to rule 37A, 42, 43, or Section 17(5) provisions.
7. Table 5 – Exempt/nil-rated supplies: Enter the value of exempt, nil-rated, and non-GST inward supplies
8. Table 6 – Payment of tax: The system calculates your tax liability (outward tax minus eligible ITC). Pay any balance using the electronic cash ledger (deposit via challan before filing).
9. Open the "Tax Liability Breakup" tab on the payment page and click SAVE (mandatory from February 2026 onwards)
10. Preview the return: Review all tables for accuracy before submission
11. File the return: Click "Submit" followed by "File Return with DSC" or "File Return with EVC"

GSTR-3B Due Dates

GSTR-3B Late Fees

Interest at 18% per annum applies on the outstanding tax amount from the due date until actual payment. For late reporting of output tax, interest is charged from the due date of the return. For excess ITC claimed, interest at 24% per annum applies from the date of utilization until reversal.

GSTR-9: Annual Return

Who Must File GSTR-9

• Mandatory: All regular GST-registered taxpayers with aggregate turnover exceeding INR 2 crore
• Exempt: Taxpayers with aggregate turnover up to INR 2 crore (from FY 2024-25 onwards)
• GSTR-9C (Reconciliation Statement): Mandatory self-certification for taxpayers with turnover above INR 5 crore. This reconciles figures between audited financial statements and GST returns.

Most foreign subsidiaries operating in India will exceed the INR 2 crore threshold and must file GSTR-9. Those above INR 5 crore must also file GSTR-9C.

Structure of GSTR-9

The GSTR-9 form is divided into 6 parts with 19 tables:

Pre-Filing Checklist

Before starting GSTR-9 preparation, complete these reconciliation steps:

• Ensure all GSTR-1 and GSTR-3B returns for the financial year are filed. GSTR-9 cannot be filed if any monthly/quarterly return is pending.
• Reconcile GSTR-1 (outward supply values) with GSTR-3B (summary values). Any differences must be identified and documented.
• Reconcile input tax credit claimed in GSTR-3B with GSTR-2B statements received from suppliers
• Reconcile turnover reported in GST returns with your audited financial statements
• Identify any invoices or credit notes that were reported in the wrong period and need adjustment
• Calculate any ITC that needs to be reversed (blocked credits under Section 17(5), proportional reversal for exempt supplies)

Step-by-Step: Filing GSTR-9 on the GST Portal

1. Log in to gst.gov.in and navigate to Services > Returns > Annual Return
2. Select the financial year and click Search
3. Under the GSTR-9 tile, click "Prepare Online"
4. Tables 4-5 (Outward/Inward Supplies): The system auto-populates values from your filed GSTR-1 and GSTR-3B returns. Review each line item: taxable supplies, exempt supplies, nil-rated supplies, non-GST supplies, advances, and their respective tax amounts.
5. Tables 6-8 (ITC Details): Review the auto-populated ITC figures. Table 6 shows ITC availed during the year. Table 7 shows ITC reversed. Table 8 reconciles ITC from GSTR-2B with ITC claimed in GSTR-3B.
6. Table 9 (Tax Paid): Review the tax payment breakup showing amounts paid through ITC and cash for IGST, CGST, SGST, and Cess
7. Tables 10-14 (Amendments): Enter any amendments to previous year's supply/ITC that were reported in the current year's returns
8. Tables 15-16 (Demands & Refunds): Report any demands raised, refunds claimed/sanctioned, and pending refunds
9. Tables 17-18 (HSN Summary): Table 17 requires HSN-wise summary of outward supplies. Table 18 requires HSN-wise summary of inward supplies. Enter the HSN code, description, UQC (unit), quantity, taxable value, and tax amounts for the top items by value.
10. Table 19 (Late Fee): If filing after the due date, the system auto-calculates the applicable late fee
11. Compute liabilities: Click "Compute Liabilities" to calculate any additional tax payable based on differences between GSTR-1/3B and GSTR-9
12. Preview and download: Click "Preview Draft GSTR-9" to review the complete return. Download a PDF for internal records.
13. File the return: Pay any additional liability through the "Create Challan" option, then click "File GSTR-9" with DSC or EVC

GSTR-9 Due Date and Penalties

The due date for GSTR-9 for FY 2024-25 is 31st December 2025. For FY 2025-26, it would be 31st December 2026 (subject to extension).

Reconciliation Tips for Foreign Companies

Foreign subsidiaries face unique reconciliation challenges that domestic companies typically do not encounter:

Transfer Pricing and Intercompany Invoices

If your Indian subsidiary receives services from or provides services to the foreign parent company, these intercompany transactions are subject to transfer pricing rules. Ensure that:

• Intercompany invoices are properly reflected in GSTR-1 (for outward) or purchase records (for inward)
• Import of services from the parent company triggers reverse charge GST—report this in GSTR-3B Table 3.1(d)
• GST paid on reverse charge for imported services is available as ITC (provided the services are used for taxable supplies)

Foreign Currency Invoicing

If your subsidiary invoices in foreign currency (common for export of services), the GST portal requires values in INR. Use the RBI reference exchange rate on the date of invoice or, if not available, the rate published by CBIC. Maintain a currency conversion log for audit purposes.

Section 15CA/15CB and GST Overlap

Remittances to the foreign parent for services require both Form 15CA/15CB (for withholding tax compliance) and proper GST treatment. These are separate compliance requirements. A payment for imported services triggers:

• TDS/withholding tax under Section 195 of the Income Tax Act
• Reverse charge GST under Section 9(3) or 9(4) of the CGST Act
• Form 15CA/15CB filing before the remittance

Common Mistakes That Trigger GST Notices

Mismatch Between GSTR-1 and GSTR-3B

The most common trigger for GST notices is a discrepancy between GSTR-1 (sales details) and GSTR-3B (summary). If your GSTR-1 shows sales of INR 50 lakh but GSTR-3B reports only INR 45 lakh, the system flags an automatic discrepancy notice. Reconcile these two returns every month before filing.

Overclaiming ITC

Claiming more ITC in GSTR-3B than what appears in your GSTR-2B (auto-generated from suppliers' GSTR-1) triggers Rule 36(4). From January 2022, ITC claims cannot exceed the amount auto-populated in GSTR-2B plus 5% tolerance. Interest at 24% per annum applies on excess ITC from the date of utilization.

Not Reporting Reverse Charge Liability

Foreign subsidiaries frequently fail to report reverse charge GST on:

• Services received from the parent company or overseas vendors
• Legal services from individual advocates
• Transportation services from goods transport agencies
• Rent paid to unregistered landlords

Missing the Three-Year Filing Window

From July 2025 onwards, GST returns cannot be filed after three years from their due date. This means returns for earlier periods (e.g., October 2022 monthly returns, FY 2020-21 annual returns) become permanently unfiled if missed, resulting in frozen non-compliance on your GST record.

Tools and Utilities for Efficient GST Filing

GST Offline Tools

The GST portal provides offline utilities for bulk data preparation, which are essential for businesses with high invoice volumes:

• GSTR-1 Offline Tool: Download the JSON template, fill invoice data in the Excel workbook, generate the JSON file, and upload it to the portal. This is faster than manual entry for businesses with hundreds of invoices per month.
• GSTR-9 Offline Tool: Useful for preparing the annual return offline, especially for reconciling large volumes of data across 19 tables.
• Returns Offline Tool (ROT): A unified tool that supports offline preparation of GSTR-1, GSTR-3B, and GSTR-9, available for download from the GST portal.

Third-Party GST Software

Most foreign subsidiaries use accounting software like Tally Prime, Zoho Books, SAP, or QuickBooks that can auto-generate GSTR-1 and GSTR-3B from accounting entries. These tools pull invoice data directly from your books, reconcile with GSTR-2B, flag mismatches, and generate the return filing JSON—significantly reducing manual effort and error risk. ClearTax and other compliance platforms offer end-to-end GST filing with automated reconciliation.

E-Invoicing Integration

If your subsidiary's turnover exceeds INR 5 crore, you must generate e-invoices through the Invoice Registration Portal (IRP) before issuing any B2B invoice. The e-invoice system automatically pushes invoice data to both the GSTR-1 portal and the buyer's GSTR-2B, eliminating manual B2B data entry in GSTR-1. This is one of the most effective ways to reduce filing errors and ensure data consistency across returns.

Practical Filing Calendar for Foreign Subsidiaries

Key Takeaways

• GSTR-1 reports outward supply details (due 11th of following month), GSTR-3B is the summary return where you pay tax (due 20th), and GSTR-9 is the annual reconciliation (due 31st December)
• Late fees range from INR 20-200 per day depending on the return type, with caps between INR 500 and 0.25% of turnover. Interest at 18% applies on unpaid tax from the due date.
• From November 2025, Table 3.2 of GSTR-3B is auto-populated and non-editable. From July 2025, returns cannot be filed after three years from their due date.
• Foreign subsidiaries must pay special attention to reverse charge on imported services, transfer pricing adjustments, and foreign currency conversion in GST returns
• Reconcile GSTR-1 and GSTR-3B every month before filing—mismatches are the single most common trigger for automated GST notices
• Engage a tax advisory firm with cross-border experience for GSTR-9 preparation, as the annual return requires reconciliation across GST, income tax, and FEMA compliance frameworks