GSTR-9 annual return for FY 2025-26: who files, the ₹2 crore exemption, GSTR-9C and a worked reconciliation
Who must file GSTR-9 and GSTR-9C for FY 2025-26, the 31 December 2026 due date, how to reconcile books with returns table by table, late fees and what software and CAs charge.
For FY 2025-26, the GSTR-9 annual return is due by 31 December 2026 for regular taxpayers whose aggregate turnover exceeded ₹2 crore; those up to ₹2 crore are exempt from FY 2024-25 onwards under Notification 15/2025-Central Tax. Taxpayers with turnover above ₹5 crore must also file GSTR-9C, a self-certified reconciliation statement. GSTR-9 is mostly auto-populated from GSTR-1 and GSTR-3B, but it is your last chance to report missed supplies and to check that your books, returns and input tax credit agree. The portal enabled GSTR-9 and GSTR-9C for FY 2025-26 in October 2026, and the tile appears only after all GSTR-1 and GSTR-3B returns for the year are filed.
This guide is part of the GST calculation worked examples section, and builds on monthly ITC reconciliation with GSTR-2B. Figures are illustrative.
Who files what
| Taxpayer | GSTR-9 | GSTR-9C |
|---|---|---|
| Regular taxpayer, aggregate turnover up to ₹2 crore | Exempt (FY 2024-25 onwards) | No |
| Regular taxpayer, ₹2 crore to ₹5 crore | Yes | No |
| Regular taxpayer above ₹5 crore | Yes | Yes, self-certified |
| Composition taxpayer | No (files GSTR-4) | No |
| Casual, non-resident, ISD, TDS deductors, TCS collectors | No | No |
Aggregate turnover is computed on an all-India basis for the PAN, but GSTR-9 is filed for each GSTIN.
What GSTR-9 contains
| Part | Content | Main source |
|---|---|---|
| Part I | Basic details | Registration |
| Part II | Outward and inward supplies on which tax is payable, for the year | GSTR-1, GSTR-3B |
| Part III | ITC availed, reversed and ineligible | GSTR-3B, GSTR-2B |
| Part IV | Tax paid as declared in returns | GSTR-3B |
| Part V | Transactions of the year declared in returns of the next year (up to the time limit) | GSTR-1/3B of April–October/November |
| Part VI | Other information: demands, refunds, HSN summary, late fee | Various |
In 2025 the form and rules were updated (Notifications 13/2025 and 16/2025-Central Tax) to reflect IMS-based ITC and new reversal disclosures. Check the current table instructions on the portal before filing.
A worked reconciliation (illustrative)
A Coimbatore pump manufacturer, single GSTIN, FY 2025-26 turnover ₹3.2 crore. The accountant compares three sources:
| Item | Books of account | GSTR-1 (total for year) | GSTR-3B (total for year) |
|---|---|---|---|
| Taxable outward supplies | ₹3,20,00,000 | ₹3,18,40,000 | ₹3,18,40,000 |
| Output tax | ₹57,60,000 | ₹57,31,200 | ₹57,31,200 |
| ITC on inputs and services | ₹41,10,000 | — | ₹41,60,000 |
| ITC per GSTR-2B for the year | — | — | ₹40,95,000 |
Finding 1: ₹1,60,000 of sales missing from returns. An invoice in March 2026 was booked but not reported in GSTR-1. Tax at 18% = ₹28,800. Since it was not reported in the year's returns, it can be reported in GSTR-9 and the tax paid through DRC-03 with interest. Interest at 18% from 21 April 2026 (the day after the March GSTR-3B was due) to, say, 15 December 2026 (239 days): ₹28,800 × 18% × 239 ÷ 365 ≈ ₹3,394.
Finding 2: ITC claimed in GSTR-3B exceeds GSTR-2B by ₹65,000. Of this, ₹50,000 relates to a supplier who filed late: the invoice was claimed in the March 2026 GSTR-3B but appeared only in the April 2026 GSTR-2B. Strictly, credit should be claimed once the invoice is in your GSTR-2B, so the accountant checks that it was not claimed a second time in April and takes advice on whether interest arises for the early claim. ₹15,000 relates to a supplier who never filed. That ₹15,000 should be reversed with interest unless the supplier files and it appears in your GSTR-2B.
Finding 3: ITC in books is ₹50,000 lower than GSTR-3B. This is the same late-filing supplier: the invoice was booked in April 2026, but ITC was claimed in March. It is a timing difference to explain in the reconciliation working papers.
After the corrections, the accountant files GSTR-9 and, because turnover is under ₹5 crore, no GSTR-9C is required.
Late fee
Late fees for GSTR-9 depend on turnover: ₹50 a day up to ₹5 crore and ₹100 a day for ₹5–20 crore, each capped at 0.04% of turnover in the state; ₹200 a day above ₹20 crore, capped at 0.5% (CGST + SGST together). The late fee and interest guide shows worked examples, and the GST late fee calculator does the multiplication.
What it costs to prepare
| Approach | Illustrative cost | Notes |
|---|---|---|
| Self-prepare from the portal's auto-populated draft | Your time | Works if books and returns already match |
| Software reconciliation module | Often included in mid-tier plans; sometimes an add-on | Check before December |
| CA or GST practitioner, GSTR-9 only | ₹5,000–₹25,000 per GSTIN | Depends on mismatches and volume |
| CA, GSTR-9 plus GSTR-9C | ₹15,000–₹60,000+ per GSTIN | More where books need reworking |
Book your professional early: December is the peak season and fees can rise for last-minute work.
Step-by-step filing
- Ensure every GSTR-1 and GSTR-3B for the year is filed; otherwise the tile does not appear.
- Download the system-computed draft and the GSTR-9 summary from the portal.
- Reconcile turnover, tax and ITC with your books (as in the example) and with GSTR-2B.
- Pay any additional tax through DRC-03 with interest before filing.
- Fill or edit the tables, preview, and compute the late fee if any.
- File with DSC or EVC. File GSTR-9C after GSTR-9 if required.
Frequently asked questions
Can I revise GSTR-9 after filing?
No. GSTR-9 cannot be revised. Errors found later are dealt with through payment by DRC-03 or in response to department proceedings. Check carefully before filing.
I'm under ₹2 crore. Should I still reconcile?
Yes. The exemption removes the filing, not the obligation to report correctly in GSTR-1 and GSTR-3B. The year-end reconciliation still protects you against notices.
Does the three-year bar apply to GSTR-9?
Yes. Since 2025 an annual return cannot be filed more than three years after its due date.
Is GSTR-9C certified by a CA?
GSTR-9C has been self-certified by the taxpayer since FY 2020-21, but many businesses still have it prepared by a CA.
Sources
- GST portal — GSTR-9/9C filing, advisories for FY 2025-26
- CBIC GST — section 44 of the CGST Act, rule 80, Notification 15/2025-Central Tax and Notifications 13/2025 and 16/2025
