GSTR-9 Annual Return FY 2025-26: Who Must File, Deadline, and How to Get It Right

GSTR-9 is the most compressed filing in the GST calendar. It has 19 tables across 6 parts, it asks for information that should already be in your monthly returns but rarely reconciles cleanly, and it lands on December 31 right alongside year-end closings. For SMEs without a dedicated tax team, the last-week-of-December scramble is now an annual ritual.

This guide gives you the practical basics: who must file, what actually goes into the return, the common reconciliation errors, and a pre-filing checklist.

What Is GSTR-9 and Why It Exists

GSTR-9 is the annual return under GST. It is a single consolidated filing that reports:

• All your outward supplies (sales) for the financial year, split by tax rate, nature (B2B, B2C, exports, reverse charge), and whether amended.
• All your inward supplies (purchases) and the Input Tax Credit (ITC) claimed against them.
• Tax paid during the year (output tax, tax under reverse charge, interest, late fees).
• Demand and refund details raised during the year.
• HSN-wise summary of outward supplies.

The purpose is reconciliation. GSTR-9 forces the department and the taxpayer to line up monthly return data (GSTR-1 and GSTR-3B) against the actual books of accounts and flag any mismatches. Discrepancies detected here are the single biggest source of post-filing GST notices under Sections 73 and 74.

Who Must File GSTR-9 for FY 2025-26

Aggregate turnover includes taxable supplies, exempt supplies, exports, and inter-state supplies. It is PAN-level, not GSTIN-level. If you have three GSTINs across three states under one PAN with combined turnover of ₹3 crore, you must file GSTR-9 separately for each GSTIN, even if individual state turnover is below ₹2 crore.

Who is exempt regardless of turnover:

• Input Service Distributors (ISD).
• Casual Taxable Persons.
• Non-Resident Taxable Persons.
• Persons deducting TDS under Section 51 (file GSTR-7 annual, not 9).
• Persons collecting TCS under Section 52 (file GSTR-8).
• Persons under the Composition Scheme (file GSTR-9A, not 9, though GSTR-9A filing has been waived in recent years).

GSTR-9 vs GSTR-9C: The Difference

This is where most SMEs get confused.

GSTR-9 (Annual Return):

• Summary of all transactions reported during the year.
• Filed by everyone above ₹2 crore turnover.
• No external certification needed.
• Based on what you already reported in your monthly GSTR-1 and GSTR-3B.

GSTR-9C (Reconciliation Statement):

• Additional statement reconciling the GSTR-9 figures with your audited books of accounts.
• Filed only by taxpayers above ₹5 crore turnover.
• Self-certified since FY 2020-21. Before that, it required CA or CMA certification. This relaxation significantly reduced compliance cost for mid-sized SMEs.
• Focuses on explaining why numbers in GSTR-9 differ from numbers in your audited P&L.

If your turnover is ₹3 crore, you file GSTR-9 but not GSTR-9C. If your turnover is ₹8 crore, you file both, on the same portal, by the same December 31 deadline.

Due Date for FY 2025-26

The due date for GSTR-9 and GSTR-9C for FY 2025-26 is December 31, 2026. December 31, 2026 falls on a Thursday, so no holiday-shift applies.

For FY 2025-26 specifically, the CBIC has not (as of April 2026) announced any extension beyond December 31. Past years have seen extensions to February or March, but plan your timeline on the statutory December deadline and treat any extension as a bonus.

What Goes Into GSTR-9: The Six Parts

GSTR-9 has 6 parts containing 19 tables. Here is the big picture before you open the return on the portal.

Most SMEs find Parts II, III, and VI (HSN summary) the most time-consuming. Parts IV and V are typically auto-populated from the monthly returns.

Reconciliation Errors to Fix Before Filing

The five mismatches that cause 80% of GSTR-9 headaches:

1. GSTR-1 vs GSTR-3B on outward supplies. Invoices reported in GSTR-1 but missed from the tax liability in GSTR-3B, or vice versa. The common cause: credit notes and amendments reported in one return but not reflected in the other.

2. GSTR-3B vs books of accounts on tax paid. Output tax paid via GSTR-3B does not match the output tax computed from your sales register. The common cause: reverse charge liabilities not accounted for, or export zero-rated supplies incorrectly coded.

3. GSTR-2B vs ITC claimed in GSTR-3B. ITC claimed in GSTR-3B exceeds the ITC reflected in GSTR-2B. After the ITC 110% rule and subsequent tightening, any excess is technically ineligible and must be reversed in GSTR-9 Table 7.

4. HSN-wise outward summary (Table 17). The HSN summary is at 6-digit HSN level for turnover above ₹5 crore and 4-digit for turnover above ₹1.5 crore. If your sales register uses inconsistent HSN coding across months, Table 17 becomes a manual clean-up job.

5. Previous year transactions in current year returns (Part V). Invoices of FY 2024-25 reported in the April-to-September 2025 filings belong in Part V of the FY 2024-25 GSTR-9, not FY 2025-26. Misclassifying these is a common error that creates phantom liabilities.

Fix these mismatches during the year at the monthly return stage. Attempting to fix a year's worth in December is how filing extensions get requested.

Late Filing Penalty

Late filing of GSTR-9 attracts:

• ₹100 per day under CGST + ₹100 per day under SGST = ₹200 per day of default.
• Capped at 0.25% of state turnover under CGST + 0.25% under SGST = 0.5% of aggregate state turnover in total.

Worked example: A business in Maharashtra with Maharashtra-state turnover of ₹4 crore files GSTR-9 20 days late.

• Late fee per day: ₹200.
• Total late fee at 20 days: ₹4,000.
• Cap check: 0.5% of ₹4 crore = ₹2,00,000.
• Payable: ₹4,000 (below cap, so the daily computation applies).

At one month late, the late fee is ₹6,000. At six months, ₹36,000. The cap is rarely the binding constraint for SMEs, but it is why large enterprises with high state turnover do eventually see the cap matter.

On top of the late fee, any unpaid tax determined during assessment attracts interest at 18% per annum under Section 50.

Pre-Filing Checklist

Before you open the GSTR-9 utility on the GST portal, make sure you have:

• All 12 GSTR-1 returns for FY 2025-26 filed and reconciled with books.
• All 12 GSTR-3B returns filed with tax paid matching the sales register.
• GSTR-2B data downloaded for all 12 months for ITC reconciliation.
• Sales register and purchase register from your books, tallied to the GSTIN-wise view.
• HSN-wise outward sales summary at the appropriate HSN digit level (4 or 6).
• Credit notes and debit notes for the year classified correctly.
• Export documentation (LUT number, shipping bills, BRC) if you have zero-rated supplies.
• Reverse charge summary separated from regular outward and inward supplies.
• DSC or EVC ready for signing at the end of filing.

Allocate two full working days for a clean filing. One day for reconciliation, one day for data entry and validation on the portal.

Common Mistakes to Avoid

• Waiting until December. The reconciliation work should happen monthly. Treating GSTR-9 as a December-only task guarantees errors.
• Filing GSTR-9 without filing every GSTR-1 and GSTR-3B for the year. The portal will reject the annual return if any monthly return is unfiled.
• Missing amendments in Part V. Any invoice of FY 2024-25 reported in your April-to-September 2025 monthly returns goes in FY 2024-25's GSTR-9 Part V, not FY 2025-26.
• Ignoring the ITC reversal in Table 7. Excess ITC claimed must be reversed with interest. Do not leave it for a Section 73 notice later.
• Treating GSTR-9C as optional. Above ₹5 crore turnover, both GSTR-9 and GSTR-9C are mandatory. Filing only GSTR-9 leaves the taxpayer in breach.
• Wrong GSTIN filing. GSTR-9 is per-GSTIN, not per-PAN. A business with four GSTINs files four GSTR-9 returns, each with its own state turnover computation.
• Forgetting about HSN summary. Table 17 (outward HSN) and Table 18 (inward HSN) are frequently skipped or filled carelessly, triggering notices later.

Let Tax Garden Own the Annual Return

The cost of a botched GSTR-9 is rarely the late fee. It is the subsequent Section 73 or 74 notice driven by unresolved mismatches that surface in departmental scrutiny. Reconciling the year at year-end is roughly five times more expensive, in both time and consultant fees, than doing it monthly.

Explore Tax Garden's Compliance Standard plan. We reconcile your GSTR-1, GSTR-3B, GSTR-2B, and books every month, maintain a running HSN-wise summary, and file GSTR-9 and GSTR-9C in November, not December 31.

Frequently Asked Questions

My turnover is ₹1.8 crore. Do I have to file GSTR-9?

No. Filing is optional for aggregate turnover up to ₹2 crore. Voluntary filing is allowed and can help close mismatches before they become notices. If you have significant ITC claims or export turnover, voluntary filing is often worth the effort.

I have three GSTINs across three states. Do I file one GSTR-9 or three?

Three, one per GSTIN. Each state's aggregate turnover is computed at the GSTIN level for filing purposes. The ₹2 crore and ₹5 crore thresholds are applied at the PAN level to determine whether GSTR-9 and GSTR-9C are mandatory across all GSTINs.

What if my GSTR-3B understated tax and I paid the difference in a later month?

Report the additional tax paid in Table 9 of GSTR-9 and, if paid in a subsequent FY, also in Part V (Tables 10 to 13). Interest under Section 50 at 18% per annum applies for the period of delay, separately from the GSTR-9 late fee.

Can I revise GSTR-9 after filing?

No. GSTR-9 is a non-revisable return. Mistakes can only be corrected through rectification in subsequent year's GSTR-1 or GSTR-3B, or via formal representation to the jurisdictional officer. This is why pre-filing reconciliation is critical.

Is GSTR-9C still CA-certified?

No, not since FY 2020-21. GSTR-9C is now self-certified by the taxpayer. This significantly reduced the compliance cost for SMEs in the ₹5 to ₹50 crore range, but the reconciliation rigour expected is the same as under the old CA-certified regime.

My turnover is exactly ₹5 crore. Do I need to file GSTR-9C?

GSTR-9C applicability is for turnover 'exceeding ₹5 crore'. At exactly ₹5 crore, GSTR-9C is not mandatory. At ₹5,00,00,001 and above, it becomes mandatory. Keep documentation of your turnover computation in case of scrutiny.

This guide is current as of April 15, 2026. GSTR-9 and GSTR-9C turnover thresholds (₹2 crore and ₹5 crore), the December 31, 2026 due date for FY 2025-26, the ₹200-per-day / 0.5%-of-turnover late fee, and the self-certified GSTR-9C relaxation have been verified against CBIC circulars and notifications on taxinformation.cbic.gov.in, the GST portal's GSTR-9 FAQ, ClearTax, IndiaFilings, Razorpay Learn, and the ICAI Technical Guide on GSTR-9. Confirm any last-minute CBIC extension on the GST portal before filing.