GSTR-9C: Who Files It and How to Reconcile

GSTR-9C is the reconciliation statement that sits on top of the annual return, matching what you declared in GSTR-9 against what your audited books say. It used to need a chartered accountant's signature before you could file it. That requirement is gone, but the reconciliation work it asks for has not shrunk — you still have to explain every rupee of difference between GST returns and financial statements, only now the person signing off on that explanation is you. This post covers who has to file it, what changed with self-certification, what is actually inside the form, and a realistic order of operations for getting it done before the deadline.

Who has to file GSTR-9C

The trigger is aggregate turnover for the financial year exceeding ₹5 crore, computed on a PAN basis but applied GSTIN by GSTIN — read the mechanics in how aggregate turnover is calculated under GST. Cross that figure for a GSTIN in a given financial year, and GSTR-9C is due for that GSTIN for that year, regardless of whether other GSTINs under the same PAN stay below it.

This is a different question from whether you need a statutory or tax audit. GSTR-9C is a GST-specific reconciliation between GST returns and books, not the audit itself. The turnover bands that decide whether GSTR-9C applies are covered alongside the broader audit picture in GST audit and turnover limits.

The threshold has been set and adjusted by notification over the years, so treat ₹5 crore as the figure to verify rather than a constant. Check the current position on gst.gov.in or cbic-gst.gov.in before you decide a GSTIN is exempt.

Why it is self-certified now, not CA-certified

For the first few years of GST, GSTR-9C had to be certified by a chartered accountant or cost accountant who had conducted the reconciliation and signed a certificate before the taxpayer could file. The Finance Act 2021 removed that requirement. From FY 2020-21 onward, GSTR-9C is self-certified: the taxpayer prepares the reconciliation, accepts it, and files it directly, with no third-party attestation step on the portal.

Practically, this shifts the accuracy risk onto the taxpayer directly. Where the certificate used to be a second set of eyes on the reconciliation, that check is now something you have to build into your own process rather than assume happens automatically before filing.

What is inside the form

GSTR-9C has two parts, though the second is now a formality rather than a live requirement.

Part A — Reconciliation Statement. This is the substantive part. It reconciles the annual gross and taxable turnover declared in GSTR-9 against the turnover in the audited financial statements, reconciles the tax paid as per the books against tax actually paid through the returns, and reconciles input tax credit availed in the returns against ITC as per the audited books. Each mismatch needs an explanation, and where the reconciliation surfaces additional liability, that amount is declared and paid through the form.

Part B — Certification. This part historically carried the CA or CMA's certificate. Since certification was made optional by the Finance Act 2021, this part no longer functions as a mandatory sign-off for self-certified filings — the taxpayer's own certification replaces it. If you have engaged an auditor for other purposes, they may still document their review separately, but the portal does not gate submission on it.

Both parts build directly on GSTR-9, so read that form first if you have not filed it yet — the GSTR-9 annual return guide walks through its tables in the order the portal presents them.

The reconciling items that actually take the time

The line items in Part A are short. The work behind each one is not. These are the differences that show up in most reconciliations, regardless of industry:

• Unbilled revenue. Revenue recognised in the books under accrual accounting before an invoice was raised, or an invoice raised in one financial year for supply completed in another. GST follows the invoice and the time of supply rules, not the accounting entry, so these two rarely agree without adjustment.
• Credit notes and debit notes. A credit note issued after the financial year end for a supply made within it, or one that reduces value for a reason GST does not recognise as a valid adjustment, creates a gap between the book figure and the GST figure. The rules on when these are valid for GST purposes are in debit notes and credit notes under GST.
• Advances. Advances received against future supply of services are taxable at receipt under GST in specified cases, while the books may recognise them as revenue only on delivery, or as a liability that never hits the turnover line at all.
• Deemed supplies. Transactions treated as a supply under Schedule I even without consideration — stock transfers between distinct persons, gifts above the threshold to employees, assets disposed of without payment — often never appear as revenue in the books at all.
• ITC booked versus GSTR-2B. Input tax credit recorded in the purchase register or books does not automatically match what GSTR-2B allowed you to claim in the returns. Supplier delays, rejected invoices in IMS, and credit claimed on ineligible items all widen this gap. Building this reconciliation as a routine rather than a year-end scramble is covered in GSTR-2B and purchase register reconciliation.

The ₹2 crore exemption on GSTR-9 has been granted year by year through specific notifications rather than as a permanent rule, so it needs re-confirming for each financial year, including FY 2025-26, on the GST portal before you treat a small-turnover GSTIN as exempt.

What has to be filed first

GSTR-9C cannot be filed in isolation. The sequence runs the other way from how the numbers are often gathered:

1. All GSTR-1 and GSTR-3B returns for the financial year need to be filed. The portal will not let the annual return process begin until the underlying periodic returns are in.
2. GSTR-9 for the same financial year has to be filed. GSTR-9C reconciles the figures already declared in GSTR-9, so it depends on that return being final.
3. Audited financial statements for the year need to be available, since Part A reconciles GSTR-9 against them line by line.

If any periodic return for the year is still outstanding, or has crossed the point where it can no longer be filed, that affects the annual return chain as well — see the three-year bar on filing GST returns for how a missed window compounds.

Due date and late fee

GSTR-9C does not carry a separate due date from GSTR-9. Both are due by 31 December following the end of the financial year. For FY 2025-26, that is 31 December 2026, unless the government issues an extension — which has happened in several past years, usually announced close to the deadline. Do not plan around an extension; check the GST portal for the confirmed date as the filing period approaches.

A practical prep timeline

Most of the difficulty in GSTR-9C is running out of time to trace a difference back to its source, not the form itself. A rough sequence that works for an October-to-December filing window:

• Early October. Confirm all GSTR-1 and GSTR-3B for the financial year are filed with no gaps, and pull the audited financial statements or draft trial balance if the audit is still in progress.
• Mid-to-late October. Draft GSTR-9, reconciling turnover, tax and ITC at a summary level against the returns. Flag anything that looks off against books at this stage rather than waiting for GSTR-9C.
• November. File GSTR-9. Start Part A of GSTR-9C in parallel — turnover reconciliation first, since it usually surfaces the largest and most time-consuming differences (unbilled revenue, deemed supplies), then tax paid, then ITC.
• Early December. Resolve open reconciling items, compute and pay any additional liability the reconciliation surfaces, and have whoever reviews the filing sign off internally even without a mandatory portal certificate.
• Before 31 December. File GSTR-9C, and leave a buffer of a few days rather than filing on the deadline itself — portal load tends to spike in the final days of any annual return season.

One recurring source of last-minute reconciling items is supplier data that turns out to be wrong late in the process — a GSTIN that was cancelled mid-year, or a vendor who stopped filing and whose invoices never made it into your GSTR-2B. Catching that earlier in the year rather than during annual return prep is easier with routine verification; our API returns registration status and GSTR filing history in one call, at ₹0.50 per verification, so checking a supplier's standing does not have to wait for year end. More in the GST compliance calendar.

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