GSTR-9 & GSTR-9C Annual Return for FY 2025-26: Complete Filing Guide

The GST annual return filing cycle for FY 2025-26 is now open. Enabled on the GST portal on October 8, 2026, every registered taxpayer whose aggregate turnover exceeds INR 2 Crores must file GSTR-9, and those exceeding INR 5 Crores must additionally file the self-certified reconciliation statement in GSTR-9C. Both are due by December 31, 2026.

Please note that the GST portal will only allow you to generate and file your GSTR-9 once all applicable GSTR-1 and GSTR-3B returns for the FY 2025-26 period have been successfully filed. Missing the December deadline triggers daily late fees, interest liability, and potential departmental scrutiny.

This guide covers the complete filing framework – who must file, what has changed, the exact late fee structure, the ITC reconciliation deadline that precedes it, and a step-by-step compliance checklist.

Who Must File GSTR-9 and GSTR-9C?

GSTR-9: Annual Return

Mandatory for: All registered taxpayers with aggregate turnover exceeding INR 2 Crores in FY 2025-26.

Exempt from filing: Taxpayers with aggregate turnover up to INR 2 Crores are exempt from filing GSTR-9, as per the exemption notification continued for FY 2025-26. Additionally, the following categories are not required to file GSTR-9:

• Composition scheme taxpayers (they file GSTR-9A)
• Input Service Distributors (ISD)
• Non-resident taxable persons
• Persons paying TDS under Section 51
• Persons paying TCS under Section 52
• Casual taxable persons

GSTR-9C: Reconciliation Statement

Mandatory for: All registered taxpayers with aggregate turnover exceeding INR 5 Crores in FY 2025-26.

GSTR-9C is a self-certified reconciliation statement reconciling the values declared in GSTR-9 with the audited annual financial statements of the taxpayer. Since FY 2020-21, GSTR-9C is self-certified by the taxpayer – it no longer requires certification by a Chartered Accountant or Cost Accountant, though professional assistance is strongly recommended given the complexity of the reconciliation.

Due Date for FY 2025-26

The due date for filing both GSTR-9 and GSTR-9C for FY 2025-26 is December 31, 2026.

This is the statutory deadline under Section 44 of the CGST Act, 2017 read with Rule 80 of the CGST Rules, 2017. As of October 2026, no extension has been announced.

Critical Pre-Filing Deadline: ITC Reconciliation by November 30, 2026

Before filing the annual return, taxpayers must ensure that all Input Tax Credit (ITC) claims for FY 2025-26 are reconciled and any pending credit notes or debit notes are accounted for.

Under Section 16(4) of the CGST Act, the last date to claim ITC for invoices pertaining to FY 2025-26 is the due date of the GSTR-3B return for September 2026 (i.e., the return filed in October 2026) or the date of filing the annual return, whichever is earlier.

For practical purposes, the ITC cut-off for most taxpayers falls on November 30, 2026 (the extended timeline under the amended Section 16(4) as per the Finance Act, 2022, allowing ITC claims up to November 30 of the following financial year). Any ITC not claimed by this date for FY 2025-26 invoices is permanently lost.

Action Required: Complete your GSTR-2B reconciliation for all months of FY 2025-26 before November 30, 2026. Identify mismatches, follow up with suppliers for missing invoices, and file any amendments or credit/debit notes before the cut-off.

What Does GSTR-9 Contain?

GSTR-9 is divided into six parts:

Part I – Basic Details: GSTIN, legal name, trade name, and financial year.

Part II – Details of Outward and Inward Supplies: Consolidated details of all outward supplies (taxable, exempt, nil-rated, non-GST), advances received and adjusted, and inward supplies attracting reverse charge.

Part III – Details of ITC: ITC availed during the year, ITC reversed, ineligible ITC under Section 17(5), ITC reclaimed, and net ITC available. This section must reconcile with the aggregate of monthly GSTR-3B filings.

Part IV – Details of Tax Paid: Tax payable and tax paid during the financial year, broken down by IGST, CGST, SGST/UTGST, and Cess – through cash and ITC.

Part V – Particulars of Transactions for the Previous FY Declared in Returns of April to September of the Current FY: Amendments, credit notes, debit notes, and ITC availed or reversed pertaining to FY 2025-26 but reported in returns filed between April and September 2026.

Part VI – Other Information: Demands and refunds, HSN-wise summary of outward and inward supplies, and late fee payable and paid.

What Does GSTR-9C Contain?

GSTR-9C requires reconciliation across two dimensions:

Part A – Reconciliation Statement:

• Table 5: Reconciliation of gross turnover declared in the audited financial statements with the turnover declared in the annual return (GSTR-9).

• Table 7: Reconciliation of taxable turnover after adjustments.

• Table 9: Reconciliation of the rate-wise tax liability as per the reconciliation statement with the tax payable as declared in GSTR-9.

• Table 12: Reconciliation of ITC declared in the annual return with the ITC availed as per the audited financial statements.

• Table 14: Reconciliation of ITC with expenses booked in the financial statements – a critical cross-check that frequently surfaces mismatches.

Part B – Certification: Self-certification by the taxpayer that the information in Part A is true and correct.

Late Fee Structure for Delayed Filing

If GSTR-9 is filed after December 31, 2026, the following late fees apply:

For taxpayers with turnover up to INR 5 Crores:

• INR 25 per day under CGST + INR 25 per day under SGST/UTGST = INR 50 per day
• Maximum cap: 0.02% of turnover in the State/UT

For taxpayers with turnover between INR 5 Crores and INR 20 Crores:

• INR 50 per day under CGST + INR 50 per day under SGST/UTGST = INR 100 per day
• Maximum cap: 0.02% of turnover in the State/UT

For taxpayers with turnover exceeding INR 20 Crores:

• INR 100 per day under CGST + INR 100 per day under SGST/UTGST = INR 200 per day
• Maximum cap: 0.50% of turnover in the State/UT (0.25% CGST + 0.25% SGST)

These amounts accumulate from January 1, 2027, until the date of actual filing.

The Three-Year Permanent Bar on Filing

Previously, taxpayers could file delayed annual returns indefinitely by paying accumulated late fees. This is no longer the case.

Under the amendments introduced by the Finance Act, 2023 (Act 8 of 2023) to Sections 37, 39, 44, and 52 of the CGST Act – notified via Notification No. 28/2023-Central Tax dated July 31, 2023 (effective October 1, 2023), and enforced on the GST portal from October 1, 2025 – the system now imposes a strict three-year time bar on all GST returns, including GSTR-9.

A taxpayer is permanently barred from filing GSTR-9 after three years from its original due date. Once this window closes, the portal completely blocks the return submission. However, the tax liability does not disappear – leaving the taxpayer exposed to best-judgment assessment and recovery proceedings under Section 62 without the ability to utilize the self-assessment framework.

For GSTR-9 of FY 2025-26 (due December 31, 2026), the three-year window closes on December 31, 2029. But the practical consequences of delayed filing – late fees, interest, and departmental scrutiny – begin accumulating from January 1, 2027.

7-Step Compliance Checklist for FY 2025-26 Annual Return

Step 1: Reconcile GSTR-1 with Books of Accounts Compare your outward supply register with all GSTR-1 filings for FY 2025-26 (April 2025 to March 2026). Identify any invoices omitted from GSTR-1, credit notes not reported, or advances not accounted for.

Step 2: Reconcile GSTR-3B with Books of Accounts Cross-check the aggregate tax liability and ITC claimed in monthly GSTR-3B returns against your books. This is the primary source for GSTR-9 auto-population.

Step 3: Complete GSTR-2B ITC Reconciliation Match your ITC claims against the GSTR-2B statements for all 12 months. Identify supplier mismatches and resolve them before the ITC cut-off date.

Step 4: Verify Reverse Charge Transactions Ensure all inward supplies attracting reverse charge under Section 9(3) and 9(4) have been correctly reported and the corresponding tax has been paid and ITC claimed.

Step 5: Prepare HSN-wise Summary GSTR-9 requires HSN-wise details of outward and inward supplies. Ensure your accounting system captures HSN codes at the invoice level for accurate reporting.

Step 6: File GSTR-9 GSTR-9 is auto-populated from GSTR-1 and GSTR-3B filings. Review every auto-populated field, make necessary amendments, and file the return on the GST portal.

Step 7: Prepare and File GSTR-9C (If Applicable) If your turnover exceeds INR 5 Crores, prepare the reconciliation statement after your annual accounts are finalized and audited. Self-certify and file GSTR-9C along with or after GSTR-9.

The GSTR-9/9C annual return involves reconciliation across multiple data sources – GSTR-1, GSTR-3B, GSTR-2B, books of accounts, and audited financial statements. A single mismatch can trigger scrutiny notices, ITC reversals, or demand proceedings.

Mundhra Consulting Services (MCS) provides end-to-end GST annual return advisory – from pre-filing reconciliation and ITC health checks to GSTR-9C preparation and post-filing dispute resolution.

Frequently Asked Questions (FAQs)

Also Read: New GST Rate List 2026: GST Slabs and Items Rate

Also Try: Free GST Calculator: Online GST Calculator India