GSTR-9C explained: reconciling audited accounts with GST returns

Who must file

Under Section 44 and Rule 80(3), every registered person whose aggregate turnover in a financial year exceeds Rs. 5 crore must file GSTR-9C along with the annual return. Since FY 2020-21, it no longer needs certification by a chartered accountant or cost accountant; the taxpayer self-certifies it. It is filed GSTIN-wise, so each registration of a business reconciles its own figures.

For a business with several state registrations but one set of audited accounts, the turnover of each GSTIN has to be carved out of the consolidated accounts, including supplies between its own branches. This is where most of the preparation time goes.

What is reconciled

• Turnover in the audited financial statements, adjusted for unbilled revenue, advances, credit notes, deemed supplies and similar items, against turnover in GSTR-9
• Taxable turnover and tax payable rate-wise against tax declared
• Reasons for each unreconciled difference
• Additional liability arising from the reconciliation, with interest

Handling differences

Differences are normal and should be explained, for example a sale booked in the accounts in March but invoiced in April, or a branch transfer that is a supply under GST but not revenue in the books. Where the difference reveals short payment, pay it through DRC-03 with interest and show it in GSTR-9C. Unexplained gaps are a common starting point for scrutiny under ASMT-10 or a departmental audit.

Practical tips

Prepare GSTR-9C only after the accounts are audited and GSTR-9 figures are final. Keep a working file with the reconciliation for each line, because officers ask for it. GSTR-9C is not the same as an audit by the department under Section 65, which is a separate proceeding starting with ADT-01. A professional can prepare the reconciliation and support you if the department later questions it.

Get it handled for you

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This guide explains the law in general terms as of October 2026. Time limits and requirements can depend on the facts of your case and on the notice you received.