GSTR-9 and GSTR-9C for FY 2025-26: Filing Guide, Turnover Limits, Due Date and Reconciliation Checklist

 

GSTR-9 and GSTR-9C Filing for FY 2025-26: What Taxpayers Need to Know

The annual GST return season is here. The GST portal enabled filing of GSTR-9 and GSTR-9C for the financial year 2025-26 from 8 October 2026. In its advisory dated 13 October 2026, GSTN asked taxpayers to file all applicable GSTR-1 and GSTR-3B returns for FY 2025-26 to enable the annual-return filing option.

For businesses and tax professionals, this is the right time to review sales, purchases, input tax credit (ITC), tax payments and books of accounts before submitting the annual return.

1. What Is the Difference Between GSTR-9 and GSTR-9C?

Although these forms are related, they serve different purposes.

Particulars	GSTR-9	GSTR-9C
Purpose	Annual GST return	Reconciliation statement
Main information	Annual sales, purchases, ITC, tax paid and other GST details	Reconciliation of GST figures with financial statements
Turnover criteria	Generally applicable above ₹2 crore, subject to exemptions	Generally applicable when aggregate turnover exceeds ₹5 crore
Filing frequency	Annually, when applicable	Annually, along with GSTR-9, when applicable

Important: Registered persons with aggregate turnover up to ₹2 crore have been exempted from filing GSTR-9 from FY 2024-25 onwards under Notification No. 15/2025-Central Tax. GSTR-9C generally applies when aggregate turnover exceeds ₹5 crore, subject to the applicable statutory exclusions and requirements.

2. What Is the Due Date for GSTR-9 and GSTR-9C for FY 2025-26?

The normal statutory due date for filing the annual return and applicable reconciliation statement is 31 December following the end of the financial year. Therefore, the normal due date for FY 2025-26 is 31 December 2026, unless the Government extends it.

Do not wait until the last few days to begin preparing the return. Reconciliation can take time, especially when the business has multiple GST registrations, a large volume of invoices or differences between accounting records and GST returns.

3. Why Is GSTR-9 Reconciliation Important?

Many taxpayers assume that annual return filing is simply a matter of accepting the figures automatically populated on the GST portal. In practice, the figures should be reviewed carefully before filing.

For example, a business may have reported annual taxable sales of ₹1.20 crore in its accounting records, while the total reported through its filed GST returns is ₹1.18 crore.

The difference is ₹2 lakh.

That difference may arise from an omitted invoice, a credit note, an amendment, a timing difference or an accounting error. The reason should be identified and documented before the annual return is finalised.

The same review is necessary for ITC, tax payments, credit notes and other relevant disclosures.

4. Seven Checks to Complete Before Filing GSTR-9

Check 1: Reconcile Annual Sales

Compare the sales recorded in your books with the figures reported in GSTR-1 and GSTR-3B for the financial year.

Review:

• B2B and B2C supplies.

• Export and other zero-rated supplies, where applicable.

• Credit notes and debit notes.

• Amendments and adjustments.

• Taxable, exempt and non-GST supplies, as applicable.

Investigate material differences rather than carrying them forward without explanation.

Check 2: Match ITC With GSTR-2B

ITC reconciliation is one of the most important parts of annual GST compliance.

Compare the ITC recorded in your books with the relevant GSTR-2B statements and the ITC reported in GSTR-3B.

Check for missing invoices, supplier reporting differences, ineligible credit, reversals and reclaims.

Remember that credit appearing in GSTR-2B is not automatically eligible in every case. The applicable conditions and restrictions must still be satisfied.

Check 3: Review Tax Paid During the Year

Compare the tax liability reported in the returns with the actual tax payments and relevant electronic ledgers.

Check whether any differences relate to:

• IGST, CGST and SGST.

• Reverse charge mechanism (RCM).

• Interest and late fees.

• Amendments or additional liabilities.

• Payments made through the appropriate ledgers.

Any additional liability identified during annual reconciliation should be evaluated and dealt with under the applicable GST provisions.

Check 4: Review Credit Notes and Amendments

Credit notes, debit notes and amendments can affect both turnover and tax liability.

Ensure the documents recorded in the books are reflected correctly in the relevant GST returns and that the annual figures are consistent with the underlying records.

Check 5: Verify HSN-Wise Summary

Review the applicable HSN-wise summary of outward supplies and check that the values and tax amounts agree with the underlying sales records and return disclosures.

Use the requirements applicable to the taxpayer and financial year rather than relying on assumptions from previous years.

Check 6: Reconcile Books With GST Returns

Prepare a working paper showing the differences between your accounting records and the filed GST returns.

For example:

Particulars	Amount
Turnover as per books	₹1,20,00,000
Turnover as per GST returns	₹1,18,00,000
Difference requiring review	₹2,00,000

This is an illustrative example, not an actual taxpayer's data. The difference must be investigated and explained before filing.

Check 7: Review GSTR-9C Applicability

If aggregate turnover exceeds ₹5 crore, check whether GSTR-9C is required.

The reconciliation statement compares relevant GST return figures with the financial statements. Prepare the necessary reconciliation and supporting workings before filing.

5. What If the GSTR-9 or GSTR-9C Option Is Not Visible on the GST Portal?

If you cannot see the annual-return filing option for FY 2025-26, first check whether all applicable GSTR-1 and GSTR-3B returns for the financial year have been filed.

GSTN specifically highlighted this requirement in its October 2026 advisory. If the option remains unavailable after checking the pending returns, consult the official GSTN helpdesk.

Official support: GST Self-Service Helpdesk

6. Common Mistakes to Avoid During Annual Return Filing

Avoid these common errors:

• Accepting auto-populated figures without checking them.

• Ignoring differences between GSTR-1 and GSTR-3B.

• Treating every invoice in GSTR-2B as eligible ITC.

• Missing credit notes or amendments.

• Overlooking tax paid under RCM.

• Failing to document reconciliation differences.

• Waiting until the due date to start preparing the return.

A properly maintained reconciliation file can save time during filing and make it easier to answer future queries.

7. How GST Software Can Help With Annual Return Preparation

Preparing annual GST returns becomes more challenging when businesses handle thousands of invoices, multiple GST registrations and extensive ITC records.

GST compliance software can help professionals organise data, compare records, identify mismatches and prepare reconciliation workings. However, the final review and filing decisions should always be based on the applicable law and verified supporting documents.

SCIGST provides GST compliance and reconciliation capabilities designed to help tax professionals and businesses manage their GST work more efficiently.