GSTR-9 and GSTR-9C Filing Guide — GST Annual Return Rules FY 2024-25

What is GSTR-9? What is GSTR-9C?

Under Section 44 of the Central Goods and Services Tax (CGST) Act, 2017, every registered taxpayer (with limited exceptions) must furnish an annual return that consolidates their tax activity for the preceding financial year. Form GSTR-9 is the prescribed annual return — it aggregates all outward supplies, inward supplies, taxes paid, and Input Tax Credit (ITC) claimed across the year’s periodic returns (GSTR-1 + GSTR-3B). It functions as the final summarisation of the year’s filings, not a fresh assessment.

Form GSTR-9C is a separate reconciliation statement filed alongside GSTR-9 by larger taxpayers. While GSTR-9 aggregates the portal data, GSTR-9C bridges the GSTR-9 numbers to the taxpayer’s audited financial statements — identifying and explaining any variances in turnover, tax liability, or ITC between the books of account and the GST portal.

Both forms exist to enable revenue assurance: they force finance teams to conduct a comprehensive year-end closure, identify missed liabilities, reverse ineligible credits, and present a reconciled financial picture before the next year’s GSTR-1 / GSTR-3B cycle proceeds.

Applicability — turnover thresholds for FY 2024-25

The obligation to file GSTR-9 + GSTR-9C depends on the Aggregate Annual Turnover (AATO) computed at the PAN level, all-India (not GSTIN-level, not state-level).

Registered person type	AATO (FY 2024-25)	GSTR-9 required?	GSTR-9C required?
Regular taxpayer	Up to ₹2 crore	Exempt (permanent, per N/N 15/2025-CT dated 17 Sep 2025)	No
Regular taxpayer	Above ₹2 crore, up to ₹5 crore	Yes (mandatory)	No
Regular taxpayer	Above ₹5 crore	Yes (mandatory)	Yes (mandatory, self-certified)

• GSTR-9 exemption below ₹2 crore — now permanent. Until FY 2023-24, the ≤₹2 crore GSTR-9 exemption was extended year-by-year via a recurring CBIC notification (most recently Notification No. 14/2024-Central Tax dated 10 July 2024 for FY 2023-24). The CBIC restructured this from FY 2024-25 onwards via Notification No. 15/2025-Central Tax dated 17 September 2025, issued under the first proviso to Section 44(1) of the CGST Act — making the exemption permanent and ongoing. AATO ≤ ₹2 crore taxpayers may still file voluntarily if they want a clean annual position recorded.
• GSTR-9C threshold of ₹5 crore. Per Rule 80(3) of the CGST Rules (amended by Notification No. 30/2021-Central Tax dated 30 July 2021), GSTR-9C is mandatory only when AATO exceeds ₹5 crore. The threshold was raised from ₹2 crore to ₹5 crore in 2021 and has held at ₹5 crore through FY 2023-24 and FY 2024-25.
• Statutory exemptions (apply regardless of turnover): Casual Taxable Persons (CTPs), Input Service Distributors (ISDs), Non-Resident Taxable Persons (NRTPs), persons deducting tax under Section 51 (TDS), and persons collecting tax under Section 52 (TCS) are exempt from filing GSTR-9 + GSTR-9C. Composition taxpayers do not file GSTR-9 — they file Form GSTR-4 annually (combined with the quarterly CMP-08 challan-cum-statement). Form GSTR-9A (the earlier composition annual return) has been suspended since FY 2019-20.
• PAN-level aggregation rule. AATO is computed at the PAN level, not the GSTIN level. If a company has four GSTINs across four states with ₹1.5 crore turnover each, the consolidated PAN-level AATO is ₹6 crore — and consequently all four GSTINs must individually file GSTR-9 + GSTR-9C, even though no single state crossed ₹5 crore on its own.

Due date for FY 2024-25 — 31 December 2025

Section 44 stipulates that the annual return must be furnished on or before the 31st of December following the close of the financial year. For FY 2024-25 (year ending 31 March 2025), the standard due date for both GSTR-9 and GSTR-9C is 31 December 2025.

Extensions are infrequent and only granted via a specific CBIC notification (typically in response to portal disruptions or industry representations). Treat 31 December 2025 as a hard deadline.

Late fees + penalties

Late fees for GSTR-9 were rationalised by turnover slab via Notification No. 07/2023-Central Tax dated 31 March 2023, amending the operation of Section 47 of the CGST Act:

AATO slab (FY 2024-25)	Late fee per day	Maximum cap
Up to ₹5 crore	₹50 (₹25 CGST + ₹25 SGST)	0.04% of state turnover (0.02% + 0.02%)
Above ₹5 crore, up to ₹20 crore	₹100 (₹50 CGST + ₹50 SGST)	0.04% of state turnover (0.02% + 0.02%)
Above ₹20 crore	₹200 (₹100 CGST + ₹100 SGST)	0.50% of state turnover (0.25% + 0.25%)

The cap is computed state-wise (per GSTIN) using the state’s portion of turnover. A delayed GSTR-9 filing across multiple GSTINs accrues these capped fees per GSTIN.

Late or non-filing of GSTR-9C separately (when GSTR-9 is filed but the reconciliation statement is not) can additionally attract the general penalty under Section 125, up to ₹25,000.

GSTR-9 structure — the 6 parts + key tables

Form GSTR-9 is divided into 6 parts comprising 19 tables. Understanding which tables are mandatory versus optional for FY 2024-25 filings prevents unnecessary data-extraction delays.

Part	Tables	Captures
Part I	1-3	Basic details — FY, GSTIN, legal name, trade name
Part II	4-5	Outward supplies — taxable and non-taxable
Part III	6-8	Input Tax Credit (ITC) — availed, reversed, reconciled
Part IV	9	Tax paid as declared in GSTR-3B
Part V	10-14	Prior-year transactions reported in current FY
Part VI	15-19	Demands, refunds, HSN summaries, other information

Key tables in detail:

• Table 4 (Part II) — supplies on which tax is payable: B2B taxable, B2C taxable, zero-rated with payment of tax, deemed exports, and inward supplies under RCM. Mandatory.
• Table 5 (Part II) — supplies on which tax is not payable: exempt, nil-rated, non-GST supplies, and zero-rated without payment of tax. Taxpayers have the option to report exempt + nil-rated + non-GST supplies as a single consolidated “exempted” figure rather than splitting them.
• Table 6 (Part III) — ITC availed as declared in GSTR-3B. Segregation into inputs / capital goods / input services remains mandatory. Table 6A(1), introduced for FY 2024-25 GSTR-9 via Notification No. 13/2025-Central Tax dated 17 September 2025, separately captures ITC pertaining to the preceding FY (FY 2023-24) claimed during FY 2024-25 — covering imports of goods/services, RCM transactions, ISD inputs, FCM invoices, and previously blocked credits subsequently allowed. ITC re-claimed under Rule 37 / 37A in the current FY is not to be reported in Table 6A(1).
• Table 7 (Part III) — ITC reversed during the FY, with separate rows for reversals under Rule 37 (180-day non-payment to vendor), Rule 37A (vendor failed to file GSTR-3B), Rule 39, Rules 42 and 43, and Section 17(5) (blocked credits).
• Table 8 (Part III) — ITC reconciliation. Table 8A auto-populates eligible ITC from GSTR-2B (the static return), forcing a hard reconciliation against the purchase register. This switched from GSTR-2A to GSTR-2B basis for FY 2023-24 GSTR-9 onwards.
• Table 17 (Part VI) — HSN-wise summary of outward supplies. Mandatory at the 6-digit HSN level for AATO above ₹5 crore. For AATO ≤ ₹5 crore, 4-digit HSN is required for B2B and optional for B2C.
• Table 18 (Part VI) — HSN-wise summary of inward supplies. Reporting threshold mirrors Table 17.

GSTR-9C structure — the reconciliation statement

GSTR-9C is the audit-trail document connecting the audited financial statements to the GST portal.

• Part A — Reconciliation Statement
  • Table 5 — reconciles gross turnover: starts with audited turnover per the financial statements, applies +/- adjustments (unbilled revenue, advances, trade discounts, deemed supplies, branch transfers), and arrives at the turnover declared in GSTR-9.
  • Table 7 — reconciles taxable turnover by adjusting exempt + non-GST supplies out of gross turnover.
  • Table 9 — reconciles rate-wise tax liability and the amount payable; identifies short-paid tax that must be discharged via DRC-03.
  • Tables 12 + 14 — reconcile net Input Tax Credit. They bridge ITC booked in the audited accounts to ITC claimed in GSTR-9, isolating specific expense heads where credit was capitalised, blocked, or reversed.
• Part B — Self-Certification — formal declaration by the registered person verifying that the information in Part A is true, correct, and maps to the books of accounts. Signed with DSC; no external CA/CMA certification required (Finance Act 2021 change — see below).

GSTR-9 vs GSTR-9C — comparison

Parameter	Form GSTR-9	Form GSTR-9C
Objective	Consolidation of GSTR-1 + GSTR-3B for the FY	Reconciliation of GSTR-9 to audited financial statements
Applicability (FY 2024-25)	Mandatory if AATO > ₹2 crore	Mandatory if AATO > ₹5 crore
Pre-requisite	All GSTR-1 + GSTR-3B for the FY must be filed	GSTR-9 must be filed before GSTR-9C
Due date	31 December 2025 (for FY 2024-25)	31 December 2025 (for FY 2024-25)
Late fee reference	Section 47 — tiered by AATO (₹50 / ₹100 / ₹200 per day, with capped percentage of state turnover)	General penalty under Section 125 (up to ₹25,000)
Certification	Self-filed using DSC	Self-certified (no CA/CMA required since FY 2020-21)
Revision	Not permitted	Not permitted

Reconciliation methodology — practical approach

Executing the annual reconciliation requires aligning three independent datasets: the ERP books of account, the GSTR-1 + GSTR-3B returns filed during the year, and the GSTR-2B received from vendors.

1. Turnover reconciliation (Table 5 of GSTR-9C). Extract revenue from operations + other income from the audited P&L. Adjust for timing differences — subtract unbilled revenue recognised in the previous FY, add unbilled revenue recognised in the current FY. Isolate pan-India branch transfers (which do not appear in the consolidated P&L but trigger GST liability under Schedule I, paragraph 2) and map them to the relevant state GSTIN.
2. Reverse Charge Mechanism (RCM). Extract GL entries for legal fees, security services, goods transport agency, sponsorships, and other RCM-eligible expenses. Confirm that the total RCM liability was discharged in cash via GSTR-3B and that the corresponding ITC was subsequently claimed in the next eligible period. The discharge and the credit are reported in different tables — confirm both legs reconcile.
3. ITC matching (Table 8 of GSTR-9). Download consolidated GSTR-2B for the FY. Reconcile against the purchase register. Any ITC booked in the books that did not auto-populate to Table 8A (because the supplier failed to upload to GSTR-1 in time) must be evaluated — if the supplier never filed, the credit must be moved to Table 7 as a Rule 37A reversal to avoid downstream DRC-01C notices.
4. Discharge additional liabilities via DRC-03. Liabilities discovered during reconciliation — short-paid tax, missed RCM, ineligible ITC retained, supplies omitted from GSTR-1 — should not be adjusted in GSTR-9 itself (GSTR-9 reports what was actually declared during the year). Pay the additional amount via Form DRC-03 from the electronic cash ledger before filing GSTR-9. The DRC-03 reference is then disclosed in Table 9 of GSTR-9 as part of taxes paid.

Common filing errors

• Treating Table 8A as GSTR-2A-based. For FY 2023-24 GSTR-9 onwards, Table 8A explicitly sources from the static GSTR-2B, not the dynamic GSTR-2A. Reconciling against the live 2A produces continuous validation failures.
• Using next-period GSTR-3B to discharge annual-return liabilities. Additional liability discovered during GSTR-9 preparation must be paid via DRC-03, not by adjusting the subsequent month’s GSTR-3B. Mixing the two breaks the audit trail.
• Misclassifying RCM in Table 4. RCM inward supplies must be reported under Table 4G (inward supplies on which tax is payable on reverse charge basis), not under Table 4A (outward B2B). Misclassification artificially inflates declared outward turnover and triggers system mismatches.
• Skipping Table 17 HSN summary. Leaving the HSN-wise outward supplies summary blank when AATO is above ₹5 crore will block the portal submission.
• Mis-stating Part V transactions. FY 2023-24 transactions amended or paid for in FY 2024-25 must be reported in Part V (Tables 10-14) of the FY 2024-25 GSTR-9, not by retrospectively adjusting the FY 2023-24 GSTR-9. Overlapping prior-year items across two annual returns triggers reconciliation gaps.

Self-certification — what the Finance Act, 2021 changed

Historically, GSTR-9C functioned as a formal GST Audit. Section 35(5) of the CGST Act (as originally enacted) required the reconciliation statement to be audited and certified by an external Chartered Accountant or Cost Management Accountant.

The Finance Act, 2021 (Sections 110-111) omitted Section 35(5) entirely and substituted Section 44 to introduce the self-certification regime. The amendment took effect for FY 2020-21 onwards.

The change moved the certification from external CA/CMA audit to self-certification by the registered person — typically the CFO, director, partner, or authorised signatory using their DSC. This reduced external compliance costs (especially for SMEs above the ₹5 crore threshold who previously had to commission a separate GST audit) but shifted the legal liability for accuracy onto the entity’s officers. Any material misstatement in the self-certified GSTR-9C now rests with corporate officers of the entity, not with a third-party CA.

What changed for FY 2023-24 + FY 2024-25 filings

The GST Council and CBIC routinely refine the annual return formats. Key structural adjustments applicable for FY 2024-25 GSTR-9:

• Table 8A now sourced from GSTR-2B (continuing the FY 2023-24 switch) — the ITC auto-population draws from the static GSTR-2B, not the dynamic GSTR-2A.
• Table 6A(1) is new for FY 2024-25 — introduced via Notification No. 13/2025-Central Tax dated 17 September 2025. Captures prior-year ITC (FY 2023-24) claimed during FY 2024-25, distinguishing it from current-year ITC. Should reconcile to Table 13 of the FY 2023-24 GSTR-9.
• Rule 37 and 37A reversals separated in Table 7 — distinct rows for reversal due to 180-day vendor non-payment (Rule 37) and reversal due to supplier non-filing of GSTR-3B (Rule 37A introduced via Notification 26/2022-CT dated 26 December 2022). Tracked separately from Rule 42 / 43 reversals.
• HSN summary enforced at 6 digits for AATO > ₹5 crore. Earlier relief allowing consolidated HSN reporting has been phased out — the Table 17 / 18 utility now requires 6-digit HSN at the AATO above ₹5 crore threshold.
• Auto-pop of liability and ITC values from GSTR-1, 3B, and 2B continues to expand — manual editing fields are increasingly restricted, making the periodic returns the binding source of truth.

Finance teams should treat GSTR-9 preparation as a 6-week project starting in October: data extraction, reconciliation, DRC-03 settlement, and self-certification take longer than the 31 December cut-off forgives if started in late November.