GST Updates

GSTR-9 and GSTR-9C for FY 2025–26: Applicability and Reconciliation

Work out which annual GST forms apply, separate November credit corrections from December filing, and reconcile turnover and ITC with practical examples.

NRS Editorial Desk · Published 2026-10-28 · 14 min read

For FY 2025–26, covered regular taxpayers with PAN-wide aggregate turnover above ₹2 crore generally file GSTR-9; above ₹5 crore, GSTR-9C is also required. The ordinary deadline is 31 December 2026. But the normal Section 16(4) cut-off for taking eligible credit is 30 November 2026—or the actual annual-return filing date, if earlier. Finish the credit review before filing.

This guide is for owners and finance teams preparing the annual GST close across India. It brings together the filing decision, source records and three worked examples. The Kerala checklist applies the same national framework to everyday trading and service-business records; it does not create a separate local filing rule.

Who must file GSTR-9 and GSTR-9C for FY 2025–26?

Notification 15/2025 applies from FY 2024–25 onwards: the ₹2 crore relief is not limited to last year. The table is for ordinary regular taxpayers, not every type of GST registration. Section 44 excludes ISDs, TDS/TCS registrations, casual taxable persons and non-resident taxable persons; other notified exclusions can apply. Composition or mixed-status periods need their own form review.

PAN-wide turnover decides the threshold; GSTIN-wise records decide the return

Aggregate turnover includes taxable and exempt supplies, exports and inter-State supplies across India under the same PAN. GST and cess, and inward supplies on which the recipient pays reverse charge, are excluded from that definition. Keep the threshold computation separate from a single GSTIN’s annual-return working.

Illustration: a business has ₹1.60 crore aggregate-turnover contribution from its Kerala GSTIN and ₹80 lakh from its Karnataka GSTIN, with no other items. PAN-wide aggregate turnover is ₹2.40 crore. Neither GSTIN can claim the ₹2 crore exemption merely because its own figure is lower. Prepare the relevant GSTR-9 separately for each registration; ₹2.40 crore does not trigger GSTR-9C.

At the other boundary, exactly ₹5 crore is not turnover exceeding ₹5 crore. If aggregate turnover is ₹5.20 crore, the covered business crosses the GSTR-9C test even if one registration contributes only ₹30 lakh. Build a GSTIN schedule and tie its total to the PAN-wide computation before preparing the individual forms.

Why the 30 November ITC cut-off matters before the December due date

For an ordinary FY 2025–26 invoice or debit note, Section 16(4) limits taking ITC to 30 November 2026 or furnishing the relevant annual return, whichever is earlier. GSTR-9 does not itself let you take fresh credit. Appearance in GSTR-2B also does not establish every eligibility condition.

Suppose the annual return is filed on 10 November. The business should not assume it can first claim a missed FY 2025–26 invoice on 20 November merely because 30 November has not passed. Obtain a clear credit sign-off before early annual filing. Special statutory exceptions require separate examination; they should not be treated as a routine extension for every invoice.

Section 34(2) separately uses a 30 November/earlier annual-return cut-off for declaring relevant tax-adjusting credit notes. Do not treat a commercial ledger credit and a GST tax reduction as interchangeable. Identify the document, supply year and lawful adjustment route before deciding the correction.

GSTR-9 versus GSTR-9C: what should each working paper explain?

GSTR-9 brings the GST year together; GSTR-9C is the reconciliation statement linking annual-return figures with audited financial statements. Current Rule 80 requires self-certification of GSTR-9C. It should not be described as the old compulsory, separately CA-certified GST audit.

Self-certification is a responsibility, not a reason to skip the bridge. A useful file lets another reviewer trace each adjustment back to an invoice, ledger, return period and decision. A balancing entry labelled ‘annual difference’ does not explain what happened.

Collect these records before opening the annual-return form

• Prepare a GSTIN list, registration-status history, PAN-wide turnover calculation and the relevant financial statements with trial balance.
• Export the year’s filed GSTR-1/IFF, GSTR-1A where applicable, GSTR-3B, GSTR-2B and available annual-return/Table 8A document details. Keep the original files and download dates.
• Obtain sales, purchases, debit notes, credit notes, advances and journal registers, with separate tax-head columns and original invoice references.
• Keep a distinct list for imports, reverse-charge expenses, ISD credit, exports, exempt activities and stock or asset transactions that need GST review.
• Bring together electronic liability, cash and credit ledgers; relevant DRC-03 acknowledgements; refund applications; and demand/payment records.
• Identify FY 2025–26 transactions reported or corrected in FY 2026–27. Preserve the original period, reporting period and document version rather than overwriting the history.

Create one exception register with these columns: GSTIN, document number/date, financial year, books amount, return amount, difference, tax head, reason, evidence, action owner and completion date. This is a practical working-paper design, not an additional statutory form.

A five-pass reconciliation that produces an explainable result

• Pass 1 — Scope: confirm registrations, turnover threshold, taxpayer status and the financial year selected. Lock the source-file set so every person works from the same version.
• Pass 2 — Outward supplies: bridge books to outward-return summaries and tax paid in GSTR-3B. Classify differences as timing, classification, duplicates, omissions or genuine tax errors.
• Pass 3 — Credit: compare purchase/expense evidence with supplier reporting and credit actually taken. Separate ordinary domestic credit from imports, RCM, ISD, blocked amounts and reversal/reclaim histories.
• Pass 4 — Cross-year items: assign each later amendment or claim to its original year and reporting period. Keep a separate cut-off decision rather than pushing every difference into one annual-return cell.
• Pass 5 — Review: decide the correction/payment route, retain evidence and obtain approval of unresolved items before filing. Reconcile GSTR-9C where it applies and archive the submitted documents.

Auto-populated figures are a starting point for review. The portal uses GSTR-2B-based Table 8A information from FY 2023–24 onwards, but the download and the form serve different purposes. Use the selected year’s instructions; do not copy last year’s optional-table concessions into a later year without checking their scope.

Worked example 1: a ₹4 lakh sales difference is not automatically ₹4 lakh of missed sales

Assume a Kozhikode trader’s initial books show net taxable sales of ₹2.64 crore, while the outward-return total is ₹2.60 crore. The reviewer finds a ₹1 lakh duplicate book entry and a genuine ₹3 lakh March invoice omitted from both the outward return and GSTR-3B liability. Assume the omitted local supply was correctly taxable at 18%; there are no other differences.

The ₹54,000 is tax under the stated assumptions, not the total settlement cost: interest and the applicable correction/payment procedure require review. If GSTR-3B had already included the tax, the same sales mismatch would not justify paying it twice. Preserve the duplicate reversal, the genuine invoice and the return/payment trail as separate evidence.

Worked example 2: purchase-register credit is not the same as credit to claim

Assume a Manjeri service business lists ₹4,50,000 of GST on purchases and expenses. Its document review classifies ₹18,000 as blocked credit, ₹12,000 as a duplicate entry and ₹20,000 as credit belonging to another GSTIN. The balance is ₹4,00,000, still subject to all eligibility conditions. Assume ₹3,75,000 of that balance was already validly claimed.

For that ₹25,000, inspect the invoice, receipt, supplier reporting, payment conditions and time limit. Check whether it was genuinely unclaimed or was claimed and later reversed. If the records support a lawful fresh claim, use the correct return route within the applicable cut-off; entering the amount in GSTR-9 does not create credit.

Worked example 3: a supplier’s later amendment needs a document trail

An invoice in the purchase register has one taxable value in the original supplier download and a different value in a later download. Before treating the change as lost or additional credit, compare the invoice number, date, GSTIN, original reporting period, amendment period and credit-note history.

Maintain an original-to-amended record pair. Mark which version was used for the earlier claim and what action was taken afterwards. This prevents a common working-paper error: counting both the original and corrected document as separate purchases. Whether a particular amount belongs in Table 8 or a cross-year disclosure must follow the current form instructions and the actual claim history.

GSTR-9 late fees: distinguish the CGST component from the combined charge

For FY 2022–23 onwards, Notification 07/2023–Central Tax reduces the CGST annual-return late fee for specified turnover bands. The following figures show the CGST component only. Check the corresponding SGST/UTGST charge and any applicable relief before calculating the combined liability.

For example, ten days at ₹25 gives ₹250 of CGST late fee before the applicable cap. That is not a statement that the combined CGST and SGST late fee is only ₹250. A low daily figure also does not waive tax or interest arising from an unrelated error.

Where GSTR-9C is required, Circular 246/03/2025 treats the annual return as complete when both forms are furnished. Filing GSTR-9 on time but leaving required GSTR-9C pending can therefore continue the late-fee period. Do not add two independent annual-return late-fee streams, or apply an expired historical amnesty to FY 2025–26.

How to prepare and preserve the filing

• Check that applicable periodic returns for the relevant year have been furnished, then use Services → Returns → Annual Return and select FY 2025–26.
• Compare the current portal summaries with the approved exception register. Review each applicable table using that year’s instructions and retain the draft preview.
• Resolve additional liabilities through the prescribed route, with interest and payment evidence where relevant. Do not treat annual disclosure as proof that a payment was made.
• Complete signatory approval and filing; preserve the ARN, filed return, reconciliation statement where required and the working-paper version that supports them.

GSTR-9 cannot be revised through the portal after filing. If the screen reports pending returns despite your records showing filed acknowledgements, verify the GSTIN, year, return periods and processing status before changing anything. Keep the evidence and raise a portal grievance where appropriate; do not invent a duplicate filing or alter correct figures to bypass a validation.

A practical annual-GST checklist for Kerala businesses

For a Calicut trading business, begin with invoice and stock records, credit notes, sales through different channels and rate-wise reporting. For a Manjeri service business, separately identify exempt activities, taxable services, common costs and imported subscriptions. These are review prompts, not assumptions about every business in either city.

A business with multiple locations should first identify which locations share a GSTIN and which have separate registrations. A branch label in the accounts is not itself a separate GST registration. Assign each exception to the correct GSTIN before drawing a PAN-wide conclusion.

NRS and Associates can assist with GST annual-return applicability, reconciliation and filing preparation from its Calicut and Manjeri offices, including support for businesses across Malappuram district and elsewhere in India. Start with the financial year, GSTIN list, turnover schedule and the mismatch you need reviewed. Avoid sending passwords, OTPs or full tax files through an initial general enquiry.

Frequently asked questions

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

The ordinary deadline under Rule 80 is 31 December 2026. A later date requires an applicable notified extension; an income-tax or MCA filing extension does not change the GST deadline.

Is GSTR-9 mandatory below ₹2 crore turnover?

Notification 15/2025–Central Tax exempts registered persons with aggregate turnover up to ₹2 crore for the relevant financial year, from FY 2024–25 onwards. Check PAN-wide turnover and the taxpayer category before applying the exemption.

Is GSTR-9C required at exactly ₹5 crore?

Rule 80(3) uses turnover exceeding ₹5 crore. Exactly ₹5 crore does not cross that threshold; GSTR-9 can still be required. Above ₹5 crore, covered regular taxpayers need GSTR-9 and a self-certified GSTR-9C.

Is the turnover test PAN-wise or GSTIN-wise?

Aggregate turnover is measured across India for the same PAN; the applicable annual returns are prepared separately for each relevant GSTIN. A small branch cannot decide the threshold from its own turnover alone.

Can I claim missed ITC in GSTR-9?

No. GSTR-9 is not the route for taking fresh input tax credit. For ordinary FY 2025–26 invoice or debit-note claims, Section 16(4) sets 30 November 2026 or the actual annual-return filing date, whichever is earlier, subject to eligibility and any applicable exception.

Can GSTR-9 be revised after filing?

The GST portal does not provide a revised GSTR-9. Complete the review and retain the approved working papers before filing; seek advice on the appropriate remedy for an error found afterwards.

Does filing GSTR-9 stop late fees if GSTR-9C is still pending?

Where GSTR-9C is required, Circular 246/03/2025 treats the annual return as complete only after both forms are furnished. The annual-return late-fee period runs until completion; it is not two separately stacked late fees.

Is GSTR-9C still a CA-certified GST audit report?

The present Rule 80(3) requires a self-certified reconciliation statement. Professional help and audited financial statements may still be relevant, but the former separate CA/CMA certification requirement should not be presented as the current GSTR-9C rule.