GSTR-9C is due 31 December. It's where a year of reconciliation gaps lands at once

GSTR-9C sounds like an audit. It used to be one — a Chartered Accountant or Cost Accountant had to certify it, until that requirement was quietly removed in 2021. What it is now is a self-certified reconciliation statement that any business above Rs 5 crore aggregate turnover has to file by 31 December, checking your audited books against the annual return your GSTR-1 and GSTR-3B already built. This is what it actually covers, who owes it, what changed in the form this year, and why the twelve months before December matter more than the statement itself.

What changed, and why "CA-certified" is now wrong

If you still think of GSTR-9C as a "CA-certified GSTR-9C" that needs an auditor's signature and a membership number, that belief is five years out of date. Notification 30/2021-Central Tax, in force from 1 August 2021, struck "Part B Certification" out of the form entirely and rewrote Rule 80(3) to require a reconciliation statement the taxpayer signs themselves. The same package of changes omitted Section 35(5)'s GST audit requirement — via Section 110 of the Finance Act 2021, commenced the same day by Notification 29/2021-Central Tax — so there is no GST audit left to attach a certification to. Since FY 2020-21 filings, GSTR-9C has been signed by the registered person or their authorised signatory, and nobody else.

Who has to file — and it's PAN-level, not per-State

Two different thresholds apply to two different forms, and conflating them is the most common mistake here.

GSTR-9, the annual return itself, is compulsory above Rs 2 crore aggregate turnover. At or below that, Notification 15/2025-Central Tax (17 September 2025) exempts you — and this is worth flagging because most compliance calendars still describe the relief as something re-issued every year. It isn't any more: the notification reads "for the financial year 2024-25 onwards," so the Rs 2 crore exemption is now standing and needed no fresh notification for FY 2025-26.

GSTR-9C is a separate, higher bar. Rule 80(3) requires it only where aggregate turnover "exceeds five crore rupees" — strictly above Rs 5 crore, filed along with GSTR-9, on the same date, not a month later.

"Aggregate turnover" is a PAN-level, all-India figure under Section 2(6) of the CGST Act — not the turnover of any one State or Union Territory. A business running Rs 3 crore through each of two GSTINs on the same PAN has Rs 6 crore in aggregate turnover, crosses the threshold, and owes a GSTR-9C for both registrations even though neither one, taken alone, looks close to Rs 5 crore.

What GSTR-9C actually checks

FORM GSTR-9C's own comparison column is your annual return, not your monthly ones. Part II is titled, verbatim, "Reconciliation of turnover declared in audited Annual Financial Statement with turnover declared in Annual Return (GSTR-9)" — audited books turnover is checked against the GSTR-9 figure, with a free-text reason required for anything that doesn't tie out. Part III does the same for tax paid; Part IV for input tax credit.

Your monthly returns never appear as a column in GSTR-9C itself. They feed into GSTR-9 a step earlier — FORM GSTR-9's own instructions point filers back to "Table 4(A) of FORM GSTR-3B" and the year's GSTR-1 filings to build up the annual figures. So the practical effect is the one you'd expect: by the time GSTR-9C runs, any gap between your books, your GSTR-1, your GSTR-3B and your GSTR-2B has already inherited into the GSTR-9 figure GSTR-9C is now checking against your audited financials. The statement doesn't run that comparison directly — it inherits the consequence of not having closed it earlier.

Part IV reconciles input tax credit claimed across the year against what your books and expense heads support — the same ITC eligibility conditions under Section 16 that decided, invoice by invoice, whether each credit was ever valid.

The 31 December deadline

For FY 2025-26, Rule 80(1) and 80(3) both fix the due date at 31 December 2026. As of 19 August 2026, no Central Tax notification has touched Rule 80 or extended this date for FY 2025-26 — the only two Central Tax notifications issued so far this year in the Central Tax series deal with a GSTR-3B filing extension and the GST Appellate Tribunal, not the annual return. That's the position today, not a guarantee through December: the Government has moved this date by notification in past filing years (Rule 80(1A)/(3A), inserted by Notification 40/2021-Central Tax, did so for FY 2020-21), so it's worth re-checking CBIC's Central Tax notification list as December approaches.

This due date is separate from the three-year bar under Section 44(2), which permanently closes the ability to furnish an annual return at all — for FY 2025-26 that bar doesn't bite until 31 December 2029, three years out, so it isn't a live constraint this filing season. See our 3-year filing bar guide if you're carrying older unfiled periods.

The late fee runs until both forms are in

Section 47(2) of the CGST Act sets the base late fee for a delayed annual return at Rs 100 per day (CGST), capped at 0.25% of turnover in the State or Union Territory. An equal amount applies under the corresponding State GST Act, so the combined exposure runs to roughly double the CGST figure — not a flat "Rs 200 per day" written into the Central Act itself, which is how the number is often quoted.

Notification 07/2023-Central Tax caps this further, standing from FY 2022-23 onwards — again, the CGST limb; a corresponding State waiver applies under each State Act: Rs 25 per day (capped at 0.02% of turnover) for aggregate turnover up to Rs 5 crore, and Rs 50 per day (also capped at 0.02%) for turnover between Rs 5 crore and Rs 20 crore. Above Rs 20 crore there is no entry in the table, so the unwaived Section 47(2) rate — Rs 100 per day, capped at 0.25% of turnover in the State or Union Territory — applies in full.

The real trap is in how the fee attaches, not just its rate. Circular 246/03/2025-GST is explicit: where GSTR-9C is required, "the annual return under section 44" means GSTR-9 and GSTR-9C together, and the late fee is not separately charged for the two forms. Filing GSTR-9 on time doesn't stop the clock if GSTR-9C is still outstanding — one fee runs from 31 December until the later of the two filings actually lands.

What changed in the form this year

FORM GSTR-9C now has a Table 17, "Late fee payable and paid," inserted by Notification 13/2025-Central Tax with effect from 22 September 2025 — so the FY 2025-26 form itself carries a place to record what you owed and what you paid under Section 47(2).

The same notification made a taxpayer-favourable change worth knowing if you've read elsewhere that additional liability in Part V can only be paid in cash. Since 22 September 2025 the instruction reads "electronic cash ledger or electronic credit ledger," not cash alone — a genuine relaxation that most secondary summaries still haven't caught up with.

Structurally, the form runs Part I (basic details) through Part V (additional liability due to non-reconciliation); there is no Part B any more, since that was the certification block removed in 2021. Part II reconciles turnover to GSTR-9, Part III reconciles tax paid, Part IV reconciles input tax credit — each with a free-text "reasons" table for anything that doesn't tie out.

What to reconcile before you file

Because GSTR-9C's own comparison runs against GSTR-9 rather than against your monthly returns directly, the actual reconciliation work has to happen earlier — invoice by invoice, against the records that built GSTR-9 in the first place. Four checks cover most of what ends up in Part II, Part III and Part IV's "reasons" tables:

• Books turnover vs GSTR-9 turnover (Part II). Credit notes issued after year-end, advances, and supplies under reverse charge are the usual sources of a genuine, explainable gap.
• Books tax liability vs GSTR-9 tax paid (Part III). Rate misclassifications and short-payments picked up late in the year surface here — and, per the form itself (Pt. III Table 11, "Additional amount payable but not paid," and Pt. V), anything payable has to be recorded there, not just noted in a footnote.
• ITC per books vs ITC claimed in GSTR-9 (Part IV). This is where a year of GSTR-2B mismatches concentrates: credit claimed before a supplier's invoice reached 2B, credit reversed and not re-claimed, and ITC that was always ineligible under Section 17(5).
• Late fee exposure (Table 17). Once you know whether GSTR-9C is even required, work out how many days past 31 December you're likely to run, and at which turnover-band rate — the fee keeps accruing on both forms together, not on whichever one you file first.

Why this is where the year actually catches up with you

None of the individual pieces above are hard on their own. What makes GSTR-9C the moment finance teams dread is that it forces every unresolved GSTR-2B mismatch, every vendor who filed late in March, every credit note that never got booked, and every timing difference you meant to chase in Q2 and didn't — twelve months of them — onto one statement at once. This is the annual, statement-level checkpoint sitting on top of the monthly discipline covered in our GST reconciliation guide: skip that discipline through the year, and December is where it all shows up together.

Doing that reconciliation invoice by invoice, across a full financial year, after the fact, is painful to do manually — which is exactly why the better fix is closing the GSTR-1/GSTR-3B/GSTR-2B/books gap every month, rather than reconstructing twelve months of it in one December sprint.

Where Recoup fits

Recoup ties your books, GSTR-2B and GSTR-3B together continuously through the year — not in the two weeks before 31 December — so the turnover and ITC figures feeding your GSTR-9 are already reconciled, invoice by invoice, well before Part II and Part IV of GSTR-9C ask you to explain a difference. It names the specific vendor or document behind every gap as it opens, so "which of the last twelve months' mismatches are still unresolved" is a lookup at year-end, not a scramble.

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