Last reviewed: 6 November 2026. The annual return for FY 2025-26 is the final checkpoint for a year of GST data. GSTR-9 and GSTR-9C cannot be revised once filed, the credit window under Section 16(4) shuts before the due date, and differences that surface later usually surface as a notice. This guide covers who files, the dates, the late fee with worked figures, a table-by-table approach, the reconciliation that makes the numbers defensible, three worked examples and a checklist you can hand to your accounts team.
At a glance
- Who must file what
- Dates, portal status and the timeline to 31 December
- Late fee, with worked figures
- ITC: the November cut-off and Table 8A
- Table-by-table approach
- The three-way reconciliation
- Three worked examples
- GSTR-9C: what the reconciliation statement must show
- Errors that lead to notices
- Pre-filing checklist
- FAQs
1. Who must file what
The annual return is a statutory requirement under Section 44 read with Rule 80 of the CGST Rules. Whether you file GSTR-9, GSTR-9C, both or neither depends on aggregate turnover, which is computed on a PAN basis across all GSTINs of the same PAN in the country and includes exempt supplies and exports but excludes taxes and inward supplies on reverse charge.
| Aggregate turnover (PAN-wise) | GSTR-9 | GSTR-9C | Basis |
|---|---|---|---|
| Up to Rs 2 crore | Not required | Not required | Notification 15/2025-Central Tax (FY 2024-25 onwards) |
| Above Rs 2 crore, up to Rs 5 crore | Required | Not required | Section 44, Rule 80(1) |
| Above Rs 5 crore | Required | Required (self-certified) | Rule 80(1), Rule 80(3) |
| Composition taxpayers | Not applicable; annual return is filed in GSTR-4 | Not applicable | Rule 62 |
| Casual and non-resident taxable persons, ISDs, TDS/TCS deductors | Not applicable | Not applicable | Section 44 proviso |
The PAN-wise trap. A proprietor with a Mumbai GSTIN of Rs 1.4 crore and a Pune GSTIN of Rs 1.1 crore has an aggregate turnover of Rs 2.5 crore. The Rs 2 crore exemption is lost for both GSTINs, and each files its own GSTR-9. The same logic applies to the Rs 5 crore limit for GSTR-9C. The exemption also does not stop a department notice for the year, so a small taxpayer should still keep the reconciliation file even when no return is due.
A GSTIN that was regular for part of the year and moved to or from composition, or was cancelled during the year, should confirm with the portal what is enabled. Where the tile is not visible on the dashboard, the usual cause is a pending GSTR-1 or GSTR-3B for some month of the year, not a portal fault.
2. Dates, portal status and the timeline to 31 December
The statutory due date is 31 December 2026. GSTN enabled the FY 2025-26 forms on the portal from 8 October 2026 and its advisory asks taxpayers to file all GSTR-1 and GSTR-3B for the year first, since the form is built from the returns already on record. No extension had been notified when this guide was reviewed. Extensions have been given for some earlier years, but a plan that depends on one is a plan that depends on luck.
| Date | Event | What to do |
|---|---|---|
| 8 October 2026 | GSTR-9/9C tiles enabled for FY 2025-26 | Download the system-computed draft and the Table 8A file |
| 20 November 2026 | October 2026 GSTR-3B due for monthly filers | This is the last regular return that can carry FY 2025-26 credit before the 30 November cut-off; QRMP filers should check their own dates |
| 30 November 2026 | Section 16(4) cut-off for FY 2025-26 invoices and debit notes | Credit not taken in a GSTR-3B filed by this date, or before GSTR-9 is filed if earlier, lapses |
| Early December 2026 | Close reconciliation; settle differences | Pay any short-paid tax through DRC-03 with interest |
| Before 20 December 2026 | Aim to have GSTR-9 and GSTR-9C ready | Review, sign off internally, file with a margin before the last week |
| 31 December 2026 | Due date | Late fee runs per day from 1 January 2027 |
Because the November cut-off applies to credit and not to the return, filing GSTR-9 early does not help you. It can in fact hurt: if you file the annual return on 10 November, Section 16(4) treats 10 November as the cut-off for any credit you had not yet taken. Our companion note on the GST ITC deadline of 30 November 2026 sets out the clean-up that should be finished before the annual return is opened for editing.
3. Late fee, with worked figures
The late fee is levied under Section 47(2) at the reduced rates of Notification 07/2023-Central Tax. It is a per-day fee split equally between CGST and SGST (or UTGST), and it is capped as a percentage of turnover in the State or Union territory. It is additional to interest and to any tax demand.
| Aggregate turnover | Fee per day (CGST + SGST) | Cap |
|---|---|---|
| Up to Rs 5 crore | Rs 50 (Rs 25 + Rs 25) | 0.04% of turnover in the State/UT |
| Rs 5 crore to Rs 20 crore | Rs 100 (Rs 50 + Rs 50) | 0.04% of turnover in the State/UT |
| Above Rs 20 crore | Rs 200 (Rs 100 + Rs 100) | 0.5% of turnover in the State/UT |
| Illustration | Days late | Fee at per-day rate | Cap | Fee payable |
|---|---|---|---|---|
| Turnover Rs 3 crore in one State | 30 | Rs 1,500 | Rs 12,000 | Rs 1,500 |
| Turnover Rs 12 crore in one State | 45 | Rs 4,500 | Rs 48,000 | Rs 4,500 |
| Turnover Rs 30 crore in one State | 200 | Rs 40,000 | Rs 15,00,000 | Rs 40,000 |
The caps rarely bind in the first months, which is why a short delay is cheap and a long delay is not. The larger costs of a late or careless annual return are usually elsewhere: interest on tax that the reconciliation finally exposes, and a department query on figures that do not tie to GSTR-3B. Where both GSTR-9 and GSTR-9C are required, confirm on the portal how the fee is being computed for a return that is already late; do not assume.
4. ITC: the November cut-off and Table 8A
Under Section 16(4), credit on an invoice or debit note of FY 2025-26 can be taken only up to the earlier of 30 November 2026 and the date on which the annual return is furnished. GSTR-9 does not give a second chance. It reports what was already availed in GSTR-3B and compares it with what the portal shows as available.
Table 8A and GSTR-2B
The auto-populated ITC figure in Table 8A is drawn from GSTR-2B, which is the reason the Invoice Management System (IMS) matters for the annual return. An invoice you rejected or left pending in IMS during the year will not be in the figure you reconcile against, and credit claimed on it will show up as a difference. Download the Table 8A file, tie it to the purchase register invoice by invoice for the large differences, and treat the system figure as a starting point, not as the answer.
Credit that needs separate attention
- FY 2024-25 credit taken in FY 2025-26. The form separates credit of the previous year claimed in the current year. Tag these invoices in the purchase register now; they are easy to forget and hard to rebuild.
- Rule 37 and Rule 37A reversals. Credit reversed because the supplier was not paid within 180 days, or because the supplier did not file GSTR-3B, is reported in the reversal rows. These are reported separately from other reversals, so they cannot be netted away.
- Rule 42 and Rule 43. The annual true-up for FY 2025-26 on exempt supplies and capital goods was to be done in the September 2026 return. If it was not, correct it now and pay interest.
- Section 17(5) blocked credit. Motor vehicles, food and beverages, club memberships, works contract for immovable property and similar items must not sit in eligible credit. Check the ledger accounts, not only the tax invoice.
- Import IGST. Compare Bill of Entry IGST with what is in GSTR-2B. A Bill of Entry that appears in the next year's 2B is reported in the specific row for imports whose credit falls in the following period.
- Rule 86B. If your monthly taxable supplies other than exempt and zero-rated crossed Rs 50 lakh, the 1% cash payment rule may have restricted credit usage during the year. See our note on Rule 86B.
5. Table-by-table approach
Rather than starting at Table 4 and working down, start from the books and build the tax story first. The table numbers below follow the structure of the form as it has applied since FY 2024-25; confirm row labels against the instructions on the portal for the year, because GSTN tends to adjust labels and the offline tool between years.
| Part | What goes in | Source to reconcile | Frequent problem |
|---|---|---|---|
| Part II (Tables 4-5) | Outward supplies: taxable, zero-rated, exempt, nil-rated, non-GST; RCM liability; credit notes, debit notes, amendments | GSTR-1, GSTR-3B, books of accounts | Credit notes issued in the next year; advances not tracked; RCM tax shown as normal outward supply |
| Part III (Tables 6-8) | ITC availed, reversed and ineligible; comparison with 2B | GSTR-3B Table 4, GSTR-2B, purchase register | Credit claimed ahead of 2B; reversals netted; previous-year credit not tagged |
| Part IV (Table 9) | Tax paid: cash and credit | Cash and credit ledgers, GSTR-3B | Tax paid through DRC-03 not reflected |
| Part V (Tables 10-14) | Transactions of FY 2025-26 declared in the April-November 2026 returns; demands; refunds | April to November 2026 GSTR-1/3B, amendment tables | Omitted invoices of March 2026 reported in 2026-27 with no mention here |
| Part VI (Tables 15-16) | Refunds and demands; supplies received from composition dealers, deemed supply, goods sent on approval | Refund register, demand orders | Rejected refunds and pending demands left blank |
| Part VII (Tables 17-18) | HSN-wise summaries of outward and inward supplies | GSTR-1 HSN table, purchase register | HSN digit-level mismatch; advances and Schedule III items included |
Two further observations from practice. First, the rate change that took effect on 22 September 2025, when most goods and services moved to the 5% and 18% structure, means many businesses carry both old and new rates for the same HSN within the same year. Split the HSN summary by rate before and after the change, and tie each split back to GSTR-1. Second, the optional-reporting tables have historically been the ones where taxpayers leave rows blank. Read the portal instruction before concluding that a table can be skipped for the year; the position has changed from year to year.
6. The three-way reconciliation
The point of the exercise is to reach a position where books, returns and the annual return agree, or where every difference has a reason and, if tax is due, a payment.
| Reconcile | Against | Typical differences |
|---|---|---|
| Turnover in books (month-wise) | GSTR-1 and GSTR-3B | Invoices missed in one return; credit and debit notes in GSTR-1 only; advances; cut-off errors in March; unbilled revenue |
| Tax liability in GSTR-1 | Tax paid in GSTR-3B | Rate errors; IGST shown as CGST/SGST; amendments declared next year |
| ITC in books | GSTR-3B Table 4 and GSTR-2B | Supplier non-filing; invoices in 2B of a different month; blocked credit not reversed; late-booked invoices |
| RCM liability and credit | GSTR-3B Table 3.1(d) and 4(A)(2),(3) | Tax paid in cash but credit not taken, or credit taken before the cash payment |
| Annual return totals | Audited financial statements | Non-GST income; deemed supplies; provisions; branch transfers; scrap and fixed asset sales |
Do this month-wise, not annually. Annual totals that happen to agree can hide a March invoice reported in April and an April credit note reported in March. If the practice has a recurring close, the reconciliation should be built into the monthly working papers. The same discipline is what keeps an ASMT-10 scrutiny notice short when one does arrive.
7. Three worked examples
Example A: turnover difference and tax payable
| Item | Amount |
|---|---|
| Taxable turnover as per books | Rs 6,40,00,000 |
| Taxable turnover in GSTR-3B (April 2025 to March 2026) | Rs 6,32,00,000 |
| Difference | Rs 8,00,000 |
| Cause 1: sale invoice of October 2025 omitted from both GSTR-1 and GSTR-3B | Rs 5,00,000 |
| Cause 2: debit note in GSTR-1 but not in GSTR-3B | Rs 3,00,000 |
| Tax at 18% on the difference | Rs 1,44,000 |
| Interest at 18% a year, Section 50(1), from 20 November 2025 to 15 December 2026 (390 days) | About Rs 27,700 |
Tax and interest are paid in cash through DRC-03 before filing, the liability is disclosed in the relevant outward-supply and tax-payment rows, and the difference is explained in the reconciliation statement. Interest is computed from the due date of the return for the month of supply, not from the date of discovery. For a debit note, the relevant month is the month of the debit note.
Example B: ITC in books, GSTR-3B and GSTR-2B
| Item | Amount (IGST + CGST + SGST) |
|---|---|
| Eligible ITC as per books | Rs 82,40,000 |
| ITC availed in GSTR-3B for the year | Rs 80,10,000 |
| ITC in GSTR-2B (Table 8A) | Rs 78,60,000 |
| Books minus GSTR-3B (credit not yet taken) | Rs 2,30,000 |
| GSTR-3B minus GSTR-2B (credit taken beyond 2B) | Rs 1,50,000 |
Reading it. The Rs 2,30,000 of eligible but unclaimed credit is a November problem. If the invoices pertain to FY 2025-26 and are valid, they must be taken in a GSTR-3B filed by 30 November 2026, which in practice means the October 2026 return due on 20 November. After that, the credit lapses and GSTR-9 cannot recover it. The Rs 1,50,000 claimed beyond 2B needs an invoice-level review: if the supplier has not filed, the credit is exposed to a demand and, for a payment older than 180 days, to reversal under Rule 37. Reverse and disclose, or document why the credit is eligible, before the annual return goes in.
Example C: a 9C that does not tie to the accounts
| Item | Amount |
|---|---|
| Revenue per audited statement of profit and loss | Rs 14,20,00,000 |
| Less: interest, scrap sale and exempt income not liable to GST | Rs 38,00,000 |
| Add: unbilled revenue at year-end and advances received | Rs 22,00,000 |
| Turnover per annual return (expected) | Rs 14,04,00,000 |
| Turnover per annual return (actual in the return) | Rs 13,96,00,000 |
| Unreconciled difference | Rs 8,00,000 |
An unexplained Rs 8,00,000 is not a rounding issue. In the statement it must be shown with a reason: a mismatch of cut-off, a supply treated as non-GST, or an actual short declaration. Where it is a short declaration, tax and interest are paid before the statement is furnished. The point is to be able to walk a department officer from the audited accounts to the return in the same order the statement uses.
8. GSTR-9C: what the reconciliation statement must show
For turnover above Rs 5 crore, GSTR-9C reconciles the audited annual financial statements with the annual return. Since FY 2020-21 the statement is self-certified by the taxpayer; a CA or CMA certificate is no longer part of the form. That change moves responsibility entirely to the taxpayer, which is why the working papers matter more.
- Turnover. Annual turnover per audited accounts, adjusted for unbilled revenue, advances, credit notes, deemed supplies and non-GST income, to reach turnover declared in the annual return.
- Tax paid. Reconcile tax payable per the statement with tax paid, rate-wise, and show any short payment.
- ITC. Reconcile ITC per books and per the annual return, with reasons for credit not availed or ineligible. Do not collapse reasons into a single line.
- Multiple GSTINs. Audited accounts are entity-wise, the return is GSTIN-wise. Prepare GSTIN-wise trial balances that add up to the audited accounts so that each statement can stand alone.
- Keep the workpaper pack. The statement is short; the file behind it should be a proper pack with ledgers, tie-out schedules and notes.
Because the statement is self-certified, a CA or finance head signing off internally should treat the pack as the product and the filing as the by-product. If you want an outside review of the pack before filing, that is a GSTR-9 and 9C filing engagement scoped on your data and your sign-off.
9. Errors that lead to notices
- Turnover in the annual return lower than GSTR-3B without a reconciliation reason.
- ITC in GSTR-3B higher than 2B, with no reversal or explanation.
- RCM liability reported but no matching credit, or credit taken before cash payment.
- Previous-year credit taken in the current year without tagging.
- HSN summary that does not match GSTR-1 for the same year.
- Tax paid on discovery through DRC-03 but not reflected in the tax-paid rows.
- Late declaration of March 2026 sales in April 2026 or later returns and no mention in the part of the form meant for that purpose.
- Filing GSTR-9 in the first week of November, closing the credit window early.
The departmental scrutiny of annual returns typically compares GSTR-9 with GSTR-1, GSTR-3B and GSTR-2B and then asks for explanations. If the pack is already prepared, the reply is a day's work; if it is not, it is a month. For the legal sequence if a demand notice is issued, see our guide to the GST show cause notice and reply.
10. Pre-filing checklist
- Confirm that all GSTR-1 and GSTR-3B for April 2025 to March 2026 are filed and that the tile is visible on the dashboard.
- Compute PAN-wise aggregate turnover and decide whether GSTR-9 is required and whether GSTR-9C is also required for each GSTIN.
- Download GSTR-1, GSTR-3B and GSTR-2B for the full year, the system-computed GSTR-9 and the Table 8A file.
- Reconcile turnover month-wise: books, GSTR-1, GSTR-3B. List each difference with a reason and the supporting document.
- Reconcile ITC: books, GSTR-3B, GSTR-2B. Take all eligible FY 2025-26 credit in a GSTR-3B filed on or before 30 November 2026.
- Check Section 17(5), Rule 37, Rule 37A, Rule 42 and Rule 43 and the annual true-up. Fix the shortfall with interest.
- Match RCM tax paid, credit taken and the entries in the books; check import IGST against Bill of Entry data.
- Prepare HSN-wise summaries for outward and inward supplies with rate split around 22 September 2025, and tie them to GSTR-1.
- Identify April-to-November 2026 entries that relate to FY 2025-26 and place them in the transactions-of-the-previous-year rows.
- Pay any short-paid tax and interest through DRC-03 before filing and keep the challan with the pack.
- Prepare GSTR-9C (if applicable) from the audited accounts with GSTIN-wise tie-outs; record reasons for every unreconciled amount.
- Review the draft internally with a second pair of eyes, file GSTR-9, then GSTR-9C, download the filed copies, and keep the pack for the statutory period.
If you run multiple entities or a high-volume ledger, move the reconciliation into the monthly cycle instead of December. Our GST registration checklist covers the registration side; for the monthly books that make the annual return easy, see our bookkeeping service.
11. Frequently asked questions
What is the due date for GSTR-9 and GSTR-9C for FY 2025-26?
31 December 2026 under Section 44 read with Rule 80, unless the Government extends it by notification. As on 6 November 2026 we have not seen an extension notified; check the CBIC and GST portal notifications again in the second half of December.
Is GSTR-9 required if aggregate turnover is up to Rs 2 crore?
No. Notification 15/2025-Central Tax exempts registered persons with aggregate turnover up to Rs 2 crore from filing the annual return for FY 2024-25 and later years. Aggregate turnover is PAN-wise across GSTINs, so confirm the PAN total before relying on this.
Who must file GSTR-9C for FY 2025-26?
A registered person whose aggregate turnover in the year exceeds Rs 5 crore, alongside GSTR-9. It is a self-certified reconciliation statement; certification by a CA or CMA is not required. Businesses between Rs 2 crore and Rs 5 crore file GSTR-9 only.
Can input tax credit missed in FY 2025-26 be claimed through GSTR-9?
No. GSTR-9 is a disclosure return. Under Section 16(4), credit on FY 2025-26 invoices must be taken in GSTR-3B by 30 November 2026 or the date of filing GSTR-9, whichever is earlier. After that the credit is generally lost.
What is the late fee for GSTR-9?
Section 47(2) as relaxed by Notification 07/2023-Central Tax: Rs 50 a day (Rs 25 CGST + Rs 25 SGST) up to Rs 5 crore turnover, capped at 0.04% of State turnover; Rs 100 a day for Rs 5-20 crore, same 0.04% cap; Rs 200 a day above Rs 20 crore, capped at 0.5%. Interest and penalties are separate.
Can GSTR-9 or GSTR-9C be revised after filing?
No. Once filed, neither form can be revised or amended. Differences found afterwards are handled through the next GSTR-3B (where the law permits), DRC-03 or a reply to a notice, so the figures should be settled before filing.
How is extra tax found during reconciliation paid?
Through Form GST DRC-03 in cash, with interest under Section 50, before the annual return is filed. The amount is then disclosed in the relevant tables.
Do composition taxpayers, casual and non-resident taxable persons file GSTR-9?
No. Composition taxpayers file GSTR-4 for the year instead. Casual and non-resident taxable persons, input service distributors and TDS or TCS deductors are outside the annual return requirement of Section 44. A composition dealer who was a regular taxpayer for part of the year should check which return applies to each period.
Should GSTR-9 be filed before 30 November 2026?
Not as a rule. Because Section 16(4) cuts off at the earlier of 30 November or the date of filing GSTR-9, filing the annual return in November closes the window on the same day. File the return in December, after 30 November has passed and the credit clean-up is complete.
What if GSTR-9 has not been enabled or Table 8A looks wrong?
Enablement requires all FY 2025-26 GSTR-1 and GSTR-3B to be filed. Table 8A is system-populated from GSTR-2B and is not final: download the Table 8A file, reconcile it with the purchase register and enter the adjusted figures in the editable tables. Raise a helpdesk ticket for genuine portal errors.
Need a second pair of eyes on the reconciliation? We prepare GST annual return working papers and handle GSTR-9 and 9C filing for MSMEs and companies, and assist on GST notices. Talk to us with your turnover range and number of GSTINs, and we can tell you which returns apply and how much time to plan.
Disclaimer: This article is general guidance based on the law and portal position as on 6 November 2026. Due dates, exemptions and form labels can change by notification or advisory; check the current position before filing. Portal enablement details are as reported from the GSTN advisory of October 2026. It is not advice on a specific set of facts.