GSTR-9 for FY 2025-26: Who Must File and Key Deadlines

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 Section 44 of the CGST Act, read with Rule 80 of the CGST Rules. 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 return data (GSTR-1 and GSTR-3B) against the actual books of accounts and flag any mismatches. Unexplained discrepancies here are a common trigger for post-filing demand notices, which for FY 2024-25 onwards are issued under Section 74A of the CGST Act (Sections 73 and 74 apply up to FY 2023-24).

Who Must File GSTR-9 for FY 2025-26

The Rs 2 crore exemption applies from FY 2024-25 onwards under Notification 15/2025-Central Tax dated 17 September 2025.

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 Rs 3 crore, you must file GSTR-9 separately for each GSTIN, even if individual state turnover is below Rs 2 crore.

Who does not file GSTR-9 regardless of turnover:

• Input Service Distributors (ISD).
• Casual Taxable Persons.
• Non-Resident Taxable Persons.
• Persons deducting TDS under Section 51 (they file the monthly GSTR-7).
• Persons collecting TCS under Section 52 (they file the monthly GSTR-8).
• Persons under the Composition Scheme (they file the annual return in GSTR-4, due 30 June; GSTR-9A applied only up to FY 2018-19).

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 Rs 2 crore turnover.
• No external certification needed.
• Based on what you already reported in your 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 Rs 5 crore turnover.
• Self-certified since FY 2020-21 (Finance Act, 2021 and Notification 30/2021-Central Tax). Before that, it required CA or CMA certification.
• Focuses on explaining why numbers in GSTR-9 differ from numbers in your audited P&L.

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

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.

Past years have occasionally seen extensions by notification, but plan your timeline on the statutory December deadline and treat any extension as a bonus. Confirm on the GST portal close to the date.

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. Relevant cells of Tables 4, 5, 6, 8 and 9 are auto-populated from GSTR-1/1A/IFF, GSTR-2B and GSTR-3B; Part V has to be worked out from your own records.

From FY 2024-25, Notification 13/2025-Central Tax added new rows such as Table 6A1 (ITC of the preceding year availed in the current year), Table 7A1 (reversal under Rule 37A) and Table 8H1 (IGST on imports availed in the next year).

Reconciliation Errors to Fix Before Filing

The five mismatches that cause most 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. Since 1 January 2022, Section 16(2)(aa) and Rule 36(4) allow ITC only on invoices that appear in GSTR-2B (the old 5% or 10% provisional credit no longer exists). Any excess claimed must be reversed or paid back with interest through DRC-03, and disclosed in the GSTR-9 ITC tables.

4. HSN-wise outward summary (Table 17). The HSN summary is at 6-digit level where aggregate turnover in the preceding year was above Rs 5 crore, and 4-digit level up to Rs 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-October 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 deadlines get missed.

Late Filing Penalty

Late fee for GSTR-9 is levied under Section 47(2) of the CGST Act and, from FY 2022-23 onwards, reduced by Notification 7/2023-Central Tax:

Worked example: A business registered only in Maharashtra, with aggregate turnover and Maharashtra turnover of Rs 4 crore, files GSTR-9 20 days late.

• Late fee per day: Rs 50.
• Total late fee at 20 days: Rs 1,000.
• Cap check: 0.04% of Rs 4 crore = Rs 16,000.
• Payable: Rs 1,000 (below cap, so the daily computation applies).

At 30 days late, the late fee is Rs 1,500. At 180 days, Rs 9,000. The Rs 16,000 cap is reached only after 320 days. The late fee is paid in cash and cannot be set off against ITC.

On top of the late fee, any tax short-paid for the year attracts interest at 18% per annum under Section 50(1). Where ITC was wrongly availed and utilised, interest under Section 50(3) is also 18% (Notification 13/2017-Central Tax as amended by Notification 9/2022-Central Tax).

Pre-Filing Checklist

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

• All GSTR-1 (or IFF and quarterly GSTR-1 under QRMP) returns for FY 2025-26 filed and reconciled with books.
• All GSTR-3B returns filed with tax paid matching the sales register.
• GSTR-2B data downloaded for all periods for ITC reconciliation (Table 8A is based on GSTR-2B).
• 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.
• Planning to file GSTR-9 before every GSTR-1 and GSTR-3B for the year is filed. The portal does not enable the annual return while any of these is pending.
• Missing amendments in Part V. Any invoice of FY 2024-25 reported in your April-to-October 2025 returns goes in FY 2024-25's GSTR-9 Part V, not FY 2025-26.
• Ignoring ITC reversals in Table 7. Excess ITC claimed must be reversed with interest. Do not leave it for a demand notice later.
• Treating GSTR-9C as optional. Above Rs 5 crore turnover, both GSTR-9 and GSTR-9C are mandatory. Filing only GSTR-9 leaves the annual return incomplete, and late fee keeps running until GSTR-9C is filed (Circular 246/03/2025-GST).
• 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 questions later.

Let Tax Garden Own the Annual Return

The cost of a botched GSTR-9 is rarely the late fee. It is the subsequent demand notice driven by unresolved mismatches that surface in departmental scrutiny. Reconciling a whole year in December takes far more time than doing it month by month.

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.

This guide was updated in September 2026. The GSTR-9 and GSTR-9C turnover thresholds (Rs 2 crore under Notification 15/2025-Central Tax and Rs 5 crore under Rule 80(3)), the December 31, 2026 due date for FY 2025-26, the late fee slabs under Notification 7/2023-Central Tax, and the FY 2024-25 form changes under Notification 13/2025-Central Tax have been checked against CBIC notifications and the GSTN FAQ on GSTR-9/9C. Confirm any last-minute extension on the GST portal before filing.

Frequently Asked Questions

Do I file one GSTR-9 per PAN or one per GSTIN?

GSTR-9 is filed separately for each GSTIN, but the Rs 2 crore filing threshold is tested on aggregate turnover across all GSTINs under the same PAN. So a business with three state registrations and combined turnover of Rs 3 crore must file three GSTR-9 returns, even if each state's turnover alone is below Rs 2 crore.

What late fee applies to a small business that files GSTR-9 late?

For aggregate turnover up to Rs 5 crore, the GSTR-9 late fee is Rs 50 per day (Rs 25 CGST plus Rs 25 SGST), capped at 0.04% of turnover in the state. It is Rs 100 per day between Rs 5 crore and Rs 20 crore (same 0.04% cap), and Rs 200 per day above Rs 20 crore (capped at 0.5%). For example, a Rs 4 crore business filing 20 days late pays Rs 1,000.

Can I file GSTR-9 if some GSTR-1 or GSTR-3B returns for the year are pending?

No. The portal allows GSTR-9 only after all GSTR-1 and GSTR-3B returns for that financial year have been filed. Clear any pending monthly or quarterly returns first, along with their late fees and interest, and then start the annual reconciliation. Leaving this for late December often pushes the annual return itself past the due date.

Where do FY 2025-26 invoices reported in April to October 2026 returns go?

Transactions of FY 2025-26 that were declared in the returns for April to October 2026 (the window closes on 30 November 2026), such as missed invoices, amendments or ITC claimed late, are reported in Part V (Tables 10 to 14) of the FY 2025-26 GSTR-9. They should not be included again in the FY 2026-27 annual return, or the same transaction gets counted twice.

What HSN detail does GSTR-9 need for a small business?

Table 17 of GSTR-9 needs an HSN-wise summary of outward supplies. Businesses whose aggregate turnover in the preceding year was above Rs 5 crore report at least 6-digit HSN codes, while those up to Rs 5 crore can report 4-digit codes. Table 18 covers inward supplies. Keeping HSN codes consistent in your invoicing software through the year saves a manual clean-up at annual return time.