GSTR-9 Annual Return Checklist for FY 2025-26

Q: Does the September 2025 GST rate change affect my annual return?

Yes. New rates took effect on 22 September 2025, abolishing the 12% and 28% slabs and adding a 40% rate for sin and luxury goods. FY 2025-26 therefore contains two rate structures, and Tables 9, 10, 11 and the Table 17 HSN summary have to show both, with the same HSN code appearing twice. Tobacco and pan masala moved separately on 1 February 2026. Check that your billing software recorded the change with an effective-from date rather than overwriting the rate.

A 15-page preparation checklist for the GST annual return and GSTR-9C. Who has to file, what to reconcile before you open the form, how the 22 September 2025 rate change splits your year, and exactly how late fee is charged. Every rule cited with its section, rule or notification number.

Table-by-table ITC reporting rules taken straight from GSTN's own published guidance
The FY 2025-26 rate split explained, with the billing-system test that catches it early
Late fee worked out by turnover slab, including the GSTR-9C trap most businesses miss

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Petpooja presents

GSTR-9 Annual Return Checklist

For Indian Businesses

Sections · 15-page PDF

FY 2025-26

What's Inside

What the 15-page checklist covers

Quick Reference and Applicability

The ₹2 crore and ₹5 crore thresholds, how to compute aggregate turnover across every GSTIN under one PAN, and which registrations never file at all.

Year-End Reconciliations

Books to GSTR-1, GSTR-1 to GSTR-3B, ITC to GSTR-2B, reverse charge, and the Rule 42, 43 and 37 reversals that have to be recomputed for the full year.

The FY 2025-26 Rate Split

Why this year needs two sets of rates in Tables 9, 10, 11 and 17, how credit notes across the change are treated, and a five-minute test on your billing system.

ITC Tables 6, 7, 8, 12 and 13

Table 6A1 and 6A2, why Table 8A now comes from GSTR-2B, what belongs in 8C and what does not, and the new 8H1 row for imports. Sourced from GSTN's own FAQ.

GSTR-9C Reconciliation

What Parts II to IV have to reconcile, how to write an unreconciled difference so it holds up later, and the new Table 17 for late fee.

Deadlines and Late Fee

The two dates that matter, late fee by turnover slab as CGST and SGST combined, and why filing GSTR-9 on time does not stop the clock on GSTR-9C.

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Petpooja Invoice keeps GST invoices, e-invoices and e-way bills date-stamped with the rate that applied on the day, and gives you rate-wise and HSN-wise reports all year, so the annual return is a review rather than a reconstruction.

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Why This Matters

Why FY 2025-26 Is the Hardest Annual Return Yet

Most businesses treat the GST annual return as a December job. Open the form, let it auto-populate, sign it off. That worked in earlier years. For FY 2025-26 it will not, and the reason has nothing to do with the form itself.

Your financial year ran from 1 April 2025 to 31 March 2026. On 22 September 2025, the GST rate structure changed. The 12% and 28% slabs were abolished, most goods at 12% moved to 5%, most at 28% moved to 18%, and a 40% rate arrived for sin and luxury goods. Hotel stays up to ₹7,500 a day went from 12% to 5%. Gyms, salons and barbers went from 18% to 5%.

That means one financial year, two rate structures, and an annual return that has to show both. The same HSN code appears twice in your Table 17 summary, once at the old rate and once at the new one. Tables 9, 10 and 11 need rows for rates that existed for less than six months. If you also sell tobacco or pan masala, those moved separately on 1 February 2026, so your year has three rate periods.

Here is where it usually breaks. Most billing software lets you edit the GST rate on a product without recording a date from which the change applies. If that happened in your system last September, every historical invoice now reprints at the new rate, your Table 17 will never agree with your filed GST returns, and you will spend the last week of December trying to work out why.

The second problem is a date almost nobody plans around. The last day to claim input tax credit for FY 2025-26 is 30 November 2026, under Section 16(4) of the CGST Act. The return is due a month later, on 31 December 2026. By the time most businesses sit down with the annual return and discover credit they never claimed, the door has already closed. That is not a correction you can make. It is money gone.

There is a sting in that provision worth knowing. Section 16(4) sets the cut-off as the earlier of 30 November or the date you furnish the annual return, and Section 34(2) does the same for credit notes. File GSTR-9 in October to get it off your list, and you have just closed your own November window.

There is a third problem if you sell through aggregators. Platform sales rarely tie to bank deposits without work, and the gap between what a platform reports and what reaches your account has to be reconciled before the annual return, not during it.

This checklist works backwards from those two dates. It covers who actually has to file, the reconciliations to finish before you open the form, table-by-table ITC rules taken from GSTN's own published guidance rather than from interpretation, and exactly how late fee is calculated on GSTR-9 and GSTR-9C separately. Every rule carries its section, rule or notification number so you can check it yourself.

Sample Preview

A sample of the ITC table rules inside

Here's a preview of what you'll get inside:

Table 8A now auto-fills from GSTR-2B, not GSTR-2A: it picks up FY 2025-26 documents in your GSTR-2B for the year, plus FY 2025-26 invoices reported late that appear between April and October 2026

Table 8C is only for credit you genuinely missed: credit you claimed, reversed and then reclaimed does not belong here, and putting it in creates a Table 8D difference you will not be able to explain

Table 6A1 holds last year's credit claimed this year: already included in 6A, and Rule 37 or 37A reclaims are the exception that stays out of it

Table 8B now comes only from Table 6B: Table 6H was delinked, so do not add reclaimed credit back to force a match

Additional liability is payable in cash through DRC-03: you cannot pay it through GSTR-9 itself, and it cannot be settled using input tax credit

... plus Tables 4, 5, 7, 9, 10, 11, 12, 13 and 17, the full GSTR-9C reconciliation, the FY 2025-26 rate split, and late fee by turnover slab, across 9 sections.

One note on the table references above: they follow the GSTR-9 form as notified for FY 2024-25, which is the most recent version GSTN has published detailed guidance on. GSTN says reporting for FY 2025-26 may change if the form is amended before the utility opens. The law does not change, but confirm the form layout on the GST portal when the FY 2025-26 utility goes live.

Key Stats

The numbers that decide your annual return

30 Nov 2026

The last date to claim FY 2025-26 input tax credit, or the date you file the annual return, whichever comes first. Credit found after that cannot be claimed at all, whatever your supplier does.

Source: Section 16(4), CGST Act 2017

₹50/day

Late fee for businesses up to ₹5 crore turnover, as CGST and SGST combined, capped at 0.04% of turnover in the state. It rises to ₹200 a day above ₹20 crore, and runs per registration.

Source: CBIC Notification 07/2023-Central Tax, dated 31-Mar-2023

1.51 crore

GST taxpayers in India in 2025, up from 66.5 lakh when GST began in 2017. Gross collections for FY 2024-25 were ₹22.08 lakh crore.

Source: Press Information Bureau, GST Reforms 2025, dated 04-Sep-2025

Common Mistakes

8 GSTR-9 Mistakes That Cost the Most

Treating 31 December as the deadline and missing 30 November

Under Section 16(4) of the CGST Act, the cut-off is the earlier of 30 November 2026 or the date you file the annual return. Missing credit discovered in December is a permanent loss, not a correction. Do the ITC reconciliation in October, and do not file GSTR-9 before it is finished.

Filing GSTR-9 in December and GSTR-9C in January

Under CBIC Circular 246/03/2025-GST, late fee under Section 47(2) applies to the complete annual return, and GSTR-9C is part of it. The GSTR-9C clock runs from the later of the due date or your GSTR-9 filing date. Every day between the two filings is chargeable.

Assuming the ₹2 crore exemption applies per GSTIN

It is tested on all-India, PAN-level aggregate turnover under Section 2(6). Two registrations of ₹1.5 crore each under one PAN add up to ₹3 crore, and neither is exempt.

Not checking whether the September rate change was date-versioned

If your billing system let someone edit a product's GST rate without an effective-from date, old invoices now reprint at new rates. Nothing will reconcile, and the cause is very hard to find in December. Reprint three September invoices and compare them today, and check them against the rate rules that apply to your line of business.

Putting claim-reverse-reclaim credit into Table 8C

Credit that was claimed, reversed and reclaimed belongs in Tables 6B, 7 and 6H. Table 8C is only for credit you never claimed in the year and picked up later. Mixing the two manufactures a Table 8D difference that cannot be explained.

Forcing Table 8D to nil by adjusting figures until it balances

A genuine difference, usually a supplier who never filed, is expected and easy to explain. A table balanced with adjusted numbers is not, and it is exactly what a scrutiny notice asks about two years later.

Trying to pay additional liability with input tax credit

Liability that surfaces during the annual return is payable in cash through FORM DRC-03. It cannot be paid through GSTR-9 itself and cannot be set off against credit. Pay it before filing and keep the reference with your working papers.

Leaving missing e-invoice IRNs to surface in the annual return

If you are above the e-invoicing threshold, an invoice that needed an IRN and never got one is not a valid tax invoice, and your customer's credit on it is at risk. Check that every invoice that needed an IRN actually got one before you reconcile, because the gap shows up in the annual return when it is far too late to fix cleanly.

Comparison

GSTR-9 vs GSTR-9C

Aspect	GSTR-9	GSTR-9C
What it is	Annual summary of the returns you already filed	Reconciliation of audited accounts to the annual return
Who files it	Aggregate turnover above ₹2 crore	Aggregate turnover above ₹5 crore
Due date, FY 2025-26	31 December 2026	31 December 2026, filed with the annual return
Certification	Filed by the taxpayer	Self-certified, no CA or CMA certificate since FY 2020-21
Source of data	GSTR-1, GSTR-1A, GSTR-3B and GSTR-2B, largely auto-filled	Your audited financial statements, prepared manually
Late fee clock	Runs from the due date to the date you file it	Runs from the later of the due date or your GSTR-9 filing date
Can it be revised	No	No

Swipe the table sideways to see the full comparison.

Start the annual return in October, not December

Download the free checklist and work backwards from the two dates that actually matter.

FAQ

Frequently asked questions

What is the GSTR-9 due date for FY 2025-26?

31 December 2026. Rule 80(1) of the CGST Rules requires the annual return on or before the thirty-first day of December following the financial year, and Rule 80(3) requires GSTR-9C to be filed along with it. Because the date comes from the Rules rather than an annual notification, plan for it rather than waiting to see whether an extension is announced. Extensions have been granted in some past years and not in others, usually within days of the deadline. Keep an eye on the monthly GST return calendar through the year so nothing is pending when the form opens.

Who is exempt from filing GSTR-9?

Registered persons whose aggregate turnover is up to ₹2 crore. Notification 15/2025-Central Tax, dated 17 September 2025, granted this exemption for FY 2024-25 and onwards, so it applies to FY 2025-26 without a fresh notification. Aggregate turnover is tested all-India under one PAN, not per registration. Separately, Input Service Distributors, TDS deductors under Section 51, TCS collectors under Section 52, casual taxable persons and non-resident taxable persons do not file GSTR-9 at whatever turnover.

Is GSTR-9C still audited by a Chartered Accountant?

No. Since FY 2020-21, GSTR-9C is a self-certified reconciliation statement. The requirement for a CA or CMA certificate was removed, which took out a cost but moved the responsibility onto the taxpayer. It is required where aggregate turnover exceeds ₹5 crore, under Rule 80(3) of the CGST Rules. You still reconcile your audited financial statements to the annual return, and every unreconciled difference needs a written reason that will make sense to someone reading it two years later.

What is the late fee for filing GSTR-9 late?

For aggregate turnover up to ₹5 crore it is ₹50 per day, being ₹25 CGST plus ₹25 SGST, capped at 0.04% of turnover in the state. Between ₹5 crore and ₹20 crore it is ₹100 per day with the same 0.04% cap. Above ₹20 crore the full Section 47(2) rate applies at ₹200 per day, capped at 0.5% of state turnover. These come from Notification 07/2023-Central Tax read with Section 47(2), and the fee runs per registration, so a business with four state GSTINs pays it four times. Late fee is separate from interest under Section 50 on any tax short-paid during the year.

Does the September 2025 GST rate change affect my annual return?

Yes, and this is what makes FY 2025-26 different. New rates took effect on 22 September 2025, abolishing the 12% and 28% slabs and adding a 40% rate for sin and luxury goods. Your financial year therefore contains two rate structures, and Tables 9, 10, 11 and the Table 17 HSN summary have to show both. The same HSN code appears twice, once for each period. Tobacco and pan masala moved separately on 1 February 2026, so businesses selling those have three rate periods. Check that your billing software recorded the change with an effective-from date rather than overwriting the rate, otherwise old invoices will reprint at new rates. Handling dated rate changes properly is one of the practical differences between billing software and manual billing. Our free GST calculator is useful for spot-checking individual invoices, and the rules for GST credit notes matter here too, because a credit note follows the rate of the supply it adjusts, not the rate on the day it is issued.

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