GST Updates

GSTR-9 and GSTR-9C Annual Return Filing for FY 2025-26 Is Now Live — Due 31 December, With a Portal Glitch CAs Should Know About

Published 15 Oct 2026· By Finoscape Editorial Team· Updated 15 Oct 2026· 6 min read

Every CA with a GST compliance practice knows what mid-October means: annual-return season has opened. The GST portal has enabled GSTR-9 and GSTR-9C filing for FY 2025-26 (the financial year just closed), with the statutory due date falling on 31 December 2026 under Section 44 of the CGST Act read with Rule 80 of the CGST Rules — unless extended, which has not happened as of this writing.

GSTR-9 / GSTR-9C — FY 2025-26 — KEY DATES

Annual return due 31 December 2026

Pending ITC must be claimed by 30 November 2026 — a full month earlier

Turnover ≤₹2cr: exempt • ₹2-5cr: GSTR-9 only • >₹5cr: GSTR-9 + GSTR-9C

The thresholds are unchanged from last cycle but worth restating precisely, because they decide which clients need what: taxpayers with aggregate turnover up to ₹2 crore remain exempt from GSTR-9 entirely, under Notification No. 15/2025-Central Tax (dated 17 September 2025); those above ₹2 crore and up to ₹5 crore must file GSTR-9 but not GSTR-9C; and only taxpayers above ₹5 crore turnover must file both GSTR-9 and a self-certified GSTR-9C reconciliation statement. There is a second, separate deadline embedded in the same filing cycle that’s easy to miss: under Section 16(4) of the CGST Act, any pending Input Tax Credit for FY 2025-26 must be claimed by 30 November 2026, or the date of filing the annual return, whichever is earlier — a full month before the annual return itself is due.

Sidebar: this is also the first annual-return cycle to fall after the September 2025 GST rate restructuring took effect (22 September 2025, under Notification Nos. 9/2025 and 15/2025-Central Tax (Rate)). Two rate structures will sit inside the same FY 2025-26 return — pre- and post-22 September — which makes HSN-wise and rate-wise reconciliation this cycle genuinely more involved than a routine annual filing, not merely a formality to tick off.

One more thing worth flagging before clients start filing: secondary reporting (A2Z Taxcorp LLP, 10 October; StudyCafe, 12 October) describes a portal glitch in which the system incorrectly prompts some filers for pending GSTR-1 or GSTR-3B returns even where those returns have in fact already been filed, with a GSTN clarification reportedly awaited at the time of those reports. Finoscape has not independently reproduced this glitch or located a GSTN advisory specifically addressing it — it is reported here as a secondary-sourced caveat, worth a client’s own portal check before assuming a genuine compliance gap, not as a confirmed, ongoing system fault.

Why It Matters

Annual-return season carries two traps every cycle: treating the ₹2 crore / ₹5 crore thresholds as a simple yes/no when a client’s turnover sits near either line, and missing the quieter 30 November ITC cut-off because attention is fixed on the 31 December headline date. This cycle adds a third: a two-rate-structure year that makes reconciliation genuinely more work than usual, plus a reported portal glitch that could cost a client time — or trigger an unnecessary compliance scramble — if taken at face value without checking the underlying filing status first.

Key Takeaways

GSTR-9/GSTR-9C for FY 2025-26 is now open for filing on the GST portal; statutory due date 31 December 2026 (Section 44, CGST Act, read with Rule 80, CGST Rules), unless extended.
Turnover up to ₹2 crore: exempt from GSTR-9 (Notification No. 15/2025-Central Tax, 17 September 2025). Above ₹2 crore up to ₹5 crore: GSTR-9 required, GSTR-9C not required. Above ₹5 crore: both GSTR-9 and self-certified GSTR-9C required.
Separate and earlier: pending FY 2025-26 ITC must be claimed by 30 November 2026, or the annual-return filing date, whichever is earlier (Section 16(4), CGST Act) — a full month ahead of the main due date.
This is the first annual-return cycle spanning the September 2025 GST rate restructuring (effective 22 September 2025) — HSN-wise and rate-wise reconciliation needs extra care this year.
A portal glitch wrongly flagging pending GSTR-1/3B filings has been reported by two independent secondary sources (A2Z Taxcorp, StudyCafe); not independently confirmed by Finoscape and no GSTN advisory on it was located this cycle — flagged as a caveat, not a verified ongoing fault.
Late filing fees: ₹50/day (turnover up to ₹5 crore), ₹100/day (₹5-20 crore), ₹200/day (above ₹20 crore) — per secondary reporting; verify the exact current rate on the GST portal before quoting to a client.

Practical Implications

Build the 30 November ITC cut-off into client calendars as its own, separate deadline — not as a footnote to 31 December — since missing it forecloses credit that can’t be recovered later. For any client whose FY 2025-26 turnover sits close to the ₹2 crore or ₹5 crore lines, confirm the figure precisely before assuming which form(s) apply; a borderline client wrongly treated as GSTR-9C-exempt (or vice versa) is an avoidable error. Given the mid-year rate change, build in extra reconciliation time this cycle specifically for HSN-wise and rate-wise data rather than assuming last year’s working papers can be rolled forward unchanged. If a client reports being asked for “pending” GSTR-1/3B filings that have, in fact, already been filed, have them re-verify the actual filing status on the portal before escalating.

Action Checklist

Confirm each affected client’s exact FY 2025-26 aggregate turnover before determining GSTR-9 / GSTR-9C applicability — do not assume based on prior-year figures alone.
Calendar 30 November 2026 separately from 31 December 2026 for every client with pending FY 2025-26 ITC.
Build additional time into this cycle’s reconciliation workpapers specifically for the pre-/post-22 September 2025 rate split.
Where a client hits the reported “pending GSTR-1/3B” prompt on the portal despite having filed, verify actual filing status directly on the portal before treating it as a real deficiency, and watch for a GSTN clarification on this specific issue.
Reconcile GSTR-9/9C figures against GSTR-1, GSTR-3B, and GSTR-2B before finalising — standard practice, worth restating given this cycle’s added rate-reconciliation complexity.

Relevant Sections / Notifications

Section 44, CGST Act, 2017, read with Rule 80, CGST Rules, 2017 (annual return; due date). Section 16(4), CGST Act, 2017 (ITC time limit). Notification No. 15/2025-Central Tax, dated 17 September 2025 (GSTR-9 exemption threshold). Notification Nos. 9/2025 and 15/2025-Central Tax (Rate), both dated 17 September 2025 (rate restructuring effective 22 September 2025).

FAQs

Q: Does every GST-registered business need to file GSTR-9C this cycle?
A: No. Only taxpayers with aggregate turnover above ₹5 crore for FY 2025-26 must file GSTR-9C (self-certified). Turnover up to ₹2 crore is exempt from GSTR-9 itself; above ₹2 crore up to ₹5 crore requires only GSTR-9, not GSTR-9C.

Q: If a client missed claiming some FY 2025-26 ITC, is 31 December the last date to fix it?
A: No — the real cut-off is earlier: 30 November 2026, or the date the annual return is actually filed, whichever comes first, under Section 16(4) of the CGST Act. Waiting until the 31 December annual-return deadline risks losing that credit if the return (or a prior one) is filed before 30 November.

See also Finoscape’s earlier coverage of GST Show Cause Notice limitation deadlines and ITC reversal under Rule 42/43 for the annual true-up.

This article is intended for general informational purposes only and does not constitute legal or tax advice. The reported portal glitch is sourced from secondary reporting only and has not been independently reproduced by Finoscape; readers should verify current filing status directly on the GST portal and consult a qualified Chartered Accountant for client-specific guidance. Prepared by Finoscape Editorial Team — hello@finoscape.com.