GSTR-9 and 9C for FY 2025-26: Matching Books, GSTR-1, 3B and 2B Before 31 December
GSTR-9 for FY 2025-26 is due on 31 December 2026 and is mandatory above ₹2 crore turnover; GSTR-9C is also required above ₹5 crore. Reconcile sales across books, GSTR-1 and GSTR-3B, and credit across books, GSTR-3B and GSTR-2B, rate by rate, since the year has rates before and after 22 September 2025.
The annual return is where a year of small differences adds up. Sales in your books do not match GSTR-1, credit in GSTR-3B does not match GSTR-2B, and nobody remembers why. For FY 2025-26 there is one more complication: two rate structures in the same year.
Who must file, and by when
| Aggregate turnover in FY 2025-26 | GSTR-9 | GSTR-9C |
|---|---|---|
| Up to ₹2 crore | Optional | Not required |
| Above ₹2 crore up to ₹5 crore | Mandatory | Not required |
| Above ₹5 crore | Mandatory | Mandatory (self-certified) |
Both are due on 31 December 2026. GSTR-9C is filed along with GSTR-9.
Composition taxpayers file GSTR-4 instead, and other special categories (such as non-resident taxpayers and input service distributors) do not file GSTR-9.
Late fee
| Turnover | Late fee per day (CGST + SGST) | Maximum |
|---|---|---|
| Up to ₹5 crore | ₹50 | 0.04% of turnover |
| ₹5 crore to ₹20 crore | ₹100 | 0.04% of turnover |
| Above ₹20 crore | ₹200 | 0.5% of turnover |
Why FY 2025-26 is harder
On 22 September 2025, most goods and services moved to the new 5% and 18% rates, with 40% for a small list. The 12% and 28% rates were largely removed. Your FY 2025-26 return therefore covers about six months at the old rates and six months at the new ones. Reconcile rate by rate, not just in total, or rate-wise differences will hide each other.
The four-way reconciliation
1. Sales: books against GSTR-1 and GSTR-3B
| Check | Common reason for a difference |
|---|---|
| Books vs GSTR-1 | Invoices entered after GSTR-1 was filed; credit notes not reported; B2B entered as B2C |
| GSTR-1 vs GSTR-3B | Tax paid in 3B in a different month; amendments made in later GSTR-1s |
| Rate-wise totals | Old-rate items invoiced after 22 September 2025 |
2. Credit: books against GSTR-3B and GSTR-2B
Table 8A of GSTR-9 is filled in automatically from GSTR-2B. Table 6 shows what you claimed in GSTR-3B. The difference has to be explained:
- ✓2B higher than 3B: credit you did not claim. Some of it may still be claimable before 30 November 2026.
- ✓3B higher than 2B: credit claimed without a GSTR-2B entry. Expect a question from the department.
- ✓Timing: FY 2025-26 invoices that suppliers uploaded in FY 2026-27 appear in 2B of the later year.
3. Tax paid
Match tax paid in cash and through credit with the electronic ledgers. Any DRC-03 payments made during the year for FY 2025-26 should be reported in the annual return.
4. Reversals
List reversals made under Rule 37 (supplier not paid within 180 days), Rule 37A (supplier did not file GSTR-3B), Rules 42 and 43 (exempt supplies), and blocked credit under Section 17(5).
A one-week plan
| Day | Task |
|---|---|
| 1 | Export the sales and purchase registers, rate-wise, for April 2025 to March 2026 |
| 2 | Download GSTR-1, GSTR-3B and GSTR-2B for the year, and the auto-drafted GSTR-9 |
| 3 | Reconcile sales: books, GSTR-1 and GSTR-3B, by rate |
| 4 | Reconcile credit: books, GSTR-3B and GSTR-2B (Table 8A) |
| 5 | Claim any missed credit before 30 November; pay shortfalls through DRC-03 |
| 6 | Prepare GSTR-9 and, if needed, GSTR-9C; get it reviewed |
| 7 | File, and save the working papers |
Do not file too early
Filing GSTR-9 for FY 2025-26 ends your right to claim FY 2025-26 credit. If you still have credit to claim, claim it in GSTR-3B first, then file the annual return.
Frequently asked questions
Can I correct a mistake in GSTR-9 after filing?
No. GSTR-9 cannot be revised. Get the reconciliation right before you file.
Is there a deadline after which GSTR-9 cannot be filed at all?
Yes. GST returns, including GSTR-9, cannot be filed more than three years after their due date.
Who signs GSTR-9C?
Since 2021 it is self-certified by the taxpayer. A chartered accountant's certificate is no longer required.
Sources
- ✓GSTR-9C: due date, applicability and turnover limit, ClearTax
- ✓GSTR-9 and 9C for FY 2025-26, NBA Office
- ✓GSTR-9 late fees reduced from FY 2022-23 (Notification 07/2023), Lexplosion
- ✓New GST rates from 22 September 2025, Tally
This is a summary, not legal advice. Confirm with your chartered accountant before you rely on it.
Written by
Founder, Airwix Technologies (Sleet)
Vatsal Sutariya is the founder of Airwix Technologies in Ahmedabad, the company that builds Sleet: SleetHR for HR and payroll, and Sleet Accounting for GST billing and books. He writes about GST, invoicing, business tax and choosing software for Indian businesses, and checks each rule against the official notification before it is published.
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