GSTR-9C: the GST reconciliation statement for turnover above ₹5 crore

What does GSTR-9C do?

GSTR-9C bridges two sets of numbers: what your audited accounts say and what you reported under GST. It reconciles turnover, taxable value, tax paid and input tax credit, and asks you to explain each difference and declare any additional liability arising from it.

Until FY 2019-20, a chartered accountant or cost accountant had to audit and certify GSTR-9C. The Finance Act 2021 removed that requirement, and since FY 2020-21 the taxpayer self-certifies it. Many businesses still get professional help, because the reconciliation needs knowledge of both accounting and GST adjustments.

Because GSTR-9C is self-certified, responsibility for its accuracy rests with the directors or proprietor who sign it. Officers compare it with your audited statements, income-tax return and GSTR-9, so a careless reconciliation can do more harm than good.

Who has to file it?

A registered person whose aggregate turnover for the financial year exceeds ₹5 crore must file GSTR-9C along with GSTR-9. Aggregate turnover is computed on an all-India PAN basis, but the statement is filed for each GSTIN separately, which means branch-wise accounts may be needed for multi-state businesses.

Taxpayers with turnover between ₹2 crore and ₹5 crore file only GSTR-9, and those up to ₹2 crore are exempt from both forms. Composition taxpayers, input service distributors, non-resident taxable persons and other special categories never file GSTR-9C.

Due date and how late fee works

GSTR-9C is due on the same date as GSTR-9: 31 December following the financial year. For FY 2025-26, that is 31 December 2026. You can file it with GSTR-9 or after GSTR-9 has been filed.

There is no separate late fee for GSTR-9C. CBIC Circular 246/03/2025-GST clarifies that where 9C is required, the annual return is complete only when both forms are filed, so the GSTR-9 late fee runs from the due date until the date GSTR-9C is filed. A one-time waiver applied to years up to FY 2022-23 if 9C was filed by 31 March 2025; that window has closed.

What data do you need?

The reconciliation is only as good as the GSTIN-wise accounts behind it, so allocation of revenue and expenses to each registration should be settled first. Collect these documents and working papers before you begin.

• Audited financial statements for the year, split GSTIN-wise where you have multiple registrations
• Filed GSTR-9 for the same GSTIN
• Reconciliation of turnover: unbilled revenue, advances, credit notes, deemed supplies and adjustments
• Rate-wise taxable value and tax, reflecting the rate changes of 22 September 2025
• ITC reconciliation between books, GSTR-9 Table 6 and GSTR-2B
• Reasons for each unreconciled difference and any additional tax payable

Common errors and consequences

Common errors include using consolidated company accounts without a GSTIN-wise split, leaving differences unexplained, ignoring deemed supplies such as stock transfers between branches, and declaring additional liability without paying it through DRC-03.

Not filing GSTR-9C keeps the annual return incomplete, so late fee keeps running and the GSTIN may be flagged for scrutiny. Explanations written in GSTR-9C are often quoted back in audit or demand proceedings, so write them precisely. Refogo's partner professionals can prepare GSTR-9C with GSTR-9 for a fixed fee.

Step by step

1. 1Finalise audited accounts

   Get statutory audit done and prepare GSTIN-wise trial balances.

2. 2File GSTR-9 first

   GSTR-9C can be filed only after or with GSTR-9 for the same year.

3. 3Prepare the reconciliation

   Reconcile turnover, tax and ITC between books and GSTR-9, noting reasons for each difference.

4. 4Pay additional liability

   Pay any extra tax disclosed through DRC-03 with interest.

5. 5Upload and file

   Fill GSTR-9C online or via the offline tool, attach audited statements and file with DSC or EVC.