GSTR-9 and GSTR-9C for FY 2025-26: who files, and what has to reconcile first

Short answer: GSTR-9 is due 31 December 2026 for FY 2025-26. It is required where aggregate turnover exceeds ₹2 crore, and GSTR-9C is added above ₹5 crore — self-certified, not audited. It cannot be revised, which is why the reconciliation belongs before the filing and not after.

The annual return is not another monthly return. It is a consolidation of what you already declared, and the work that decides whether it goes smoothly happens before the form is opened.

Who files, and who is outside it

Filing is exempt where aggregate turnover for the year is ₹2 crore or less — Notification No. 15/2025-Central Tax, continuing an exemption CBIC has notified every year since GST began.

Two tests operate at once, and confusing them is the most common applicability error:

• The threshold is tested on aggregate turnover across the PAN.
• The return is filed separately for each GSTIN.

So a business registered in three states with ₹80 lakh of turnover in each is at ₹2.4 crore aggregate. It is above the threshold, and it files three returns.

Six categories sit outside Section 44 regardless of turnover:

GSTR-9C, and the certification myth

Above ₹5 crore aggregate turnover, GSTR-9C is filed alongside — the statement reconciling the declared figures to the audited accounts.

It is self-certified. The Finance Act 2021 amended Section 44 to remove both the GST audit and the CA/CMA certification, with effect from FY 2020-21. A large amount of published guidance — including material written this year — still describes GSTR-9C as a certified audit. It has not been one for several years. A chartered accountant may prepare it, and usually should, but the certification on the form is the taxpayer's own.

The commercial distinction is worth holding on to: GSTR-9 summarises what you filed; GSTR-9C is where it meets the books. The second is where the differences become visible, and it is the one that takes the time.

What changed this year: Table 8A now comes from IMS

This is the substantive change for FY 2025-26, and it catches people who have filed the annual return for years without difficulty.

Table 8A — ITC available as per GSTR-2B — is now auto-populated through the Invoice Management System, rather than flowing directly from raw 2B data. IMS lets the recipient accept, reject or hold each invoice, and only accepted invoices flow through 2B into Table 8A.

The consequence: an invoice rejected in IMS does not appear in Table 8A, even where the credit is perfectly legitimate. If it was rejected in error, or rejected pending a dispute later settled with the supplier, the credit has to be reconciled manually and disclosed in the appropriate table rather than left to the auto-population.

That makes the IMS action log for the year a reconciliation input it never used to be. If nobody has been reviewing IMS actions month to month, that review is now part of the annual return exercise.

The four reconciliations to do first

This is the actual work, and doing it in October rather than late December is the difference between a two-day filing and a two-week one.

1. GSTR-1 to GSTR-3B. Output declared against output paid. A gap here is what generates the automated intimations — a shortfall in 3B against 1 is exactly the Rule 88C trigger described in the GST notice ladder. Better found now than as a DRC-01B later.
2. GSTR-3B to the books. Turnover per the trial balance against turnover declared. Differences are usually timing, credit notes, or supplies recorded net of them.
3. GSTR-2B and IMS to credit taken. The conditions that decide claimability are set out in why GSTR-2B decides what you can claim. Credit taken that never appeared in 2B is the exposure that surfaces here — and this year, credit rejected in IMS is a second category to check.
4. Rate changes falling inside the year. Where rates moved during FY 2025-26, supplies before and after the changeover carry different rates and the reconciliation has to respect the date rather than the invoice batch.

Where it goes wrong

• Treating it as data entry. The form is largely auto-populated. The value is entirely in what the auto-population disagrees with.
• Leaving it to December. There is no revision. A rushed filing is a permanent one.
• Reconciling turnover and stopping. Credit is usually where the money is.
• Ignoring a year where filing was optional. An unreconciled year does not become safe by going unfiled — and after three years, Section 44(2) closes it for good. The three-year bar and what it forecloses is covered in can't file an old GST return.

What to have ready

• GSTR-1 and GSTR-3B summaries for all twelve months
• GSTR-2B for all twelve months, and the IMS action log
• Trial balance, and the audited financial statements where available
• Electronic credit ledger and cash ledger for the year
• Credit notes issued, and details of any supplies recorded net of them
• For a multi-state business, the whole set for every GSTIN

This is a working reference, not the statute. Thresholds, the due date and the late-fee slab are all notification-driven and have been revised before — confirm the current position against the governing notification before filing.