Filing GSTR-9 and GSTR-9C vs Financial Statements – Key points to consider

Accurate filing of GSTR-9 and GSTR-9C for FY 2024-25 requires meticulous reconciliation between financial statements, GST returns, and supporting records, as these annual filings are closely scrutinized for mismatches. Taxpayers must ensure turnover reported in books aligns with GSTR-1 and GSTR-3B, properly classify taxable, exempt, nil-rated, and non-GST supplies, and correctly account for debit and credit notes. Input tax credit reconciliation is critical, including identification of ineligible ITC, reversals, and reclaims, with clear linkage to GSTR-2B and audited accounts. Tax liability under CGST, SGST, IGST, RCM, and cess must match payments made, while HSN/SAC codes, quantities, and values should be consistent to avoid audit flags. Special care is needed for advances, exports, refunds, and audit adjustments. Timely filing by 31 December 2025, along with robust documentation retained for six years, is essential to minimize disputes, late fees, and penalties. The following points can be taken into considering while preparing GSTR – 9/9C for FY 2024-25:

1. Reconcile Total Turnover

Ensure total turnover in financial statements matches taxable supplies in GSTR-1 and GSTR-3B. Include Taxable supplies under CGST/SGST/IGST, Exempted, nil-rated, and non-GST supplies. Adjust for credit notes, debit notes, and export sales. Ensure these are captured in both books and GST returns.

2. Input Tax Credit (ITC) Reconciliation

• ITC claimed in GSTR-3B should align with books of accounts. Identify and adjust:
  • ITC availed on ineligible items (e.g., personal expenses, motor vehicles for personal use)
  • ITC reversed for non-compliant suppliers
  • Reversal of ITC on exempted supplies

GSTR-9C specifically requires a column-wise reconciliation of ITC with audited accounts.

3. Verify Tax Paid and Liability

• Ensure GST liability in returns matches tax liability calculated from financial statements.
• Check CGST, SGST, IGST, and cess separately.
• Adjust for any advance tax, TDS/TCS deductions, or self-assessed liabilities.
• Ensure interest and late fees, if any, are accounted for.

4. HSN/SAC Code Verification

• HSN (goods) / SAC (services) codes in financial statements or ERP reports must match those in GSTR-9 reporting.
• Verify quantity and value details to avoid audit flags because small mismatches can trigger notices or audits.

5. Account for Debit and Credit Notes

• Ensure that all debit/credit notes issued or received are captured correctly.
• Adjust taxable turnover and ITC in GSTR-9 accordingly.

6. Segregate Exempt, Nil-Rated, and Non-GST Supplies

• Maintain separate records for these categories.
• Report these separately in GSTR-9 as required.

7. Handle Advances, Refunds, and Export Transactions Carefully

• Ensure that advances received for supplies are accounted correctly for GST.
• Reconcile export sales with financial statements and supporting export-related documentation.
• Include refund claims accurately in reconciliation.

8. Reconcile with GSTR-3B Filings

• Maintain a reconciliation worksheet: Books → GSTR-3B → GSTR-9 → GSTR-9C.
• Ensure all entries in GSTR-9 tie back to GSTR-3B filings for the financial year.
• GSTR-9C specifically checks for mismatches between audited financial statements and GSTR-3B.

9. Incorporate Audit Adjustments

• Any audit adjustments (prior period errors, omissions, or restatements) must be reflected in GSTR-9 and GSTR9C.
• Ensure sufficient documentation for any adjustments made.

10. Observe Filing Timelines

• GSTR-9: Mandatory if aggregate turnover exceeds ₹2 crore (exempt below ₹2 crore for FY 2024-25).
• GSTR-9C: Mandatory if aggregate turnover exceeds ₹5 crore (and GSTR-9 is applicable; self-certified, no external CA certification required).
• The due date for filing GSTR-9 and GSTR-9C for FY 2024-25 is December 31, 2025 (no extension announced as of December 18, 2025; late fees apply thereafter).
• Ensure timely filing to avoid late fees (₹200/day, capped at 0.5% of turnover) or penalties.

Maintain Documentation and Records

• Maintain supporting documents for all reconciliations:
  • Invoices, credit/debit notes
  • Payment receipts
  • GST payment challans
  • ITC records
  • Export documents
• Retain records for at least 6 years for audit purposes.

Tips for Smooth Filing:

• Use ERP or accounting software to generate reconciliation reports between GST returns and financial statements.
• Double-check round-off errors, small mismatches, or data entry errors, as these are commonly flagged during audits.
• Note recent changes for FY 2024-25 (e.g., enhanced ITC reporting, new tables for reversals/reclaims) and refer to GSTN FAQs or notifications for precise handling

Checklist Table for Quick Reference

Conclusion

Filing GSTR-9 and GSTR-9C accurately ensures compliance and minimizes audit risks. Businesses should reconcile turnover, ITC, and taxes carefully, verify HSN/SAC codes, maintain proper documentation, and meet deadlines. Start preparation early, especially with the tight timeline remaining until December 31, 2025.

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Disclaimer: The above information is intended for academic guidance and is to be used for informative purpose only. The said information is not to be considered as an opinion or advice. The aforesaid information is proprietary and privileged and is not to be used, reproduced and disclosed without consent. It is advisable to check with a subject matter expert before concluding on applicability or non-applicability of any compliance under any legislature. The views expressed are strictly personal.

 The above article is written by Momin Aatir Ahmed and CA Shravan Suratwala. The authors can be reached at  contact@smsuratwala.com or shravan.suratwala@outlook.com. Momin Aatir Ahmed is currently pursuing Chartered Accountancy course and is currently completing internship with S.M. Suratwala & Co., Chartered Accountants, Pune. Shravan Suratwala is a Partner at S.M. Suratwala & Co., Chartered Accountants. Shravan has 10+ years of post-qualification professional experience in advisory, litigation and compliance areas of Corporate and International taxation and Assurance. He has also worked three plus years in the field of Internal and Process Audit while pursuing chartered accountancy course.