GSTR-9 is filed per GSTIN, not per PAN. Multiple state registrations under the same company mean a separate GSTR-9 for each GSTIN — no consolidated entity-level filing.

If your GSTIN was cancelled during the financial year, you still have to file GSTR-9 for that year. No exemption applies because the registration is no longer active.

Critical New Blocking Rule from April 2026

A pending GSTR-9 for FY 2025-26 will block all your FY 2026-27 monthly GSTR-3B filings on the portal. This is not just a fine situation anymore — it is an operational lockout. Your business cannot file any monthly return for the new year until the annual return for the previous year is cleared.

Permanent Block for Returns Older Than 3 Years

From January 2026, the GST portal permanently blocks returns older than 3 years. If you have any unfiled GSTR-9 from FY 2022-23 or earlier, those are permanently lost — you can no longer file them and any associated ITC is gone for good.

IMS-Based Auto-Population of Table 8A (Big Change)

The Invoice Management System (IMS), launched in October 2024, is now a core part of your GSTR-9 preparation. Table 8A — which shows ITC as per GSTR-2B — is now auto-populated from IMS data. Every supplier invoice that you accepted, rejected, or left pending in IMS directly affects your Table 8A figure. If you rejected invoices or left them pending and those amounts remain unclaimed, they appear as a gap in Table 8D. The GSTN system may flag this as ITC leakage or potential misclassification.

Before preparing GSTR-9, review your entire IMS action history for April 2025 through March 2026. Any invoice left in pending status after the last GSTR-3B of the year is treated as deemed accepted — but without the ITC actually being claimed, it creates a reconciliation gap.

New Tables — 6A1, A1, A2, and 8H1

Four new tables were introduced via Notification No. 16/2025-Central Tax:

• Table 6A1 — A new section allowing taxpayers to present a more accurate, reconciled view of ITC claims. It breaks down ITC between amounts matching GSTR-2B and amounts claimed beyond GSTR-2B. Tax experts note this table specifically helps during desk reviews and significantly reduces the chances of scrutiny notices.
• Tables A1 and A2 — New disclosure tables for IMS-related ITC adjustments and credit note reversals under the amended Section 34.
• Table 8H1 — Captures ITC available in GSTR-2B but not claimed, giving officers a clear picture of whether unclaimed credits were intentional or an oversight.

More Detailed ITC Reversal Reporting

Notification No. 13/2025-Central Tax introduced new fields covering reversals under Rules 37, 37A, 38, 42, and 43 separately — plus re-claims in subsequent years and import-related ITC. The previous form merged several of these categories. The revised structure is, as one tax expert described, "far more detailed" — requiring businesses to maintain better documentation of each reversal type throughout the year.

Credit Note Reversal via IMS (New from October 2025)

From the October 2025 tax period, when a supplier issues a credit note, the recipient must actively accept or reject it in IMS. If you accept a credit note, you must declare whether a full or partial ITC reversal is required. This IMS-based reversal flow now feeds directly into GSTR-9 Tables 7 and Table A2.

HSN Reporting — 6-Digit Mandatory Above ₹5 Crore

For businesses with turnover above ₹5 crore, 6-digit HSN codes are mandatory in Tables 17 and 18 (outward and inward supply HSN summaries). Below ₹5 crore, 4-digit HSN is sufficient. Two-digit codes are not accepted.

Complete All Monthly/Quarterly Returns

Log in to gst.gov.in and confirm every GSTR-1 and GSTR-3B for April 2025 through March 2026 is filed and accepted. This is a hard system requirement — the portal blocks GSTR-9 preparation until all periodic returns are cleared.

Navigate to Annual Return

Go to Services → Returns → Annual Return on the GST portal. Select FY 2025-26 and click "Prepare Online" under GSTR-9.

Review IMS Dashboard Before Anything Else

This is the new Step 3 that did not exist in earlier years. Before touching any table in GSTR-9, open your IMS dashboard and review all invoice actions for FY 2025-26. Pending invoices, rejected credit notes, and IMS-accepted-but-unclaimed records will all affect Table 8A and the new 6A1 reconciliation view. Download the Table 8A Excel document detail file and reconcile each supplier record.

Review and Edit Auto-Populated Tables

Tables 4, 5, 6A, 6G, 6K, 6L, and 9 are auto-populated from your GSTR-1 and GSTR-3B filings. Review each one — auto-populated does not mean verified. Common errors include credit notes not reflected in Table 4I, zero-rated exports in wrong rows, and ISD credits missing from Table 6G.

Fill In the Remaining Sections Manually

• Table 6B–6H and new Table 6A1: ITC breakdown by category — inputs, input services, capital goods, imports, RCM, ISD. Table 6A1 captures the reconciliation between GSTR-2B available ITC and what you actually claimed.
• Table 7 (with new sub-fields): ITC reversed under Rules 37, 37A, 38, 42, 43, Section 17(5) — each now in separate rows.
• Table 8: ITC reconciliation. Table 8A (from GSTR-2B/IMS), 8B (ITC claimed in 6B+6H), 8D (gap/unclaimed ITC), 8G (IGST on imports), and new 8H1 for unclaimed ITC disclosure.
• Tables 10–14 (Most Commonly Missed Section): These capture FY 2025-26 transactions that were reported in GSTR-1 or GSTR-3B between April and November 2026 — amendments and declarations made after March 31, 2026, but before November 30, 2026. Many businesses skip these entirely, leaving an incomplete picture of their annual liability.
• Tables 15–18: Demands and refunds, composition taxpayer purchases, and HSN-wise summaries for outward and inward supplies.

Complete GSTR-9 Reconciliation (The Critical Step)

See the full reconciliation section below — this step determines whether your filing is clean or risky.

Pay Any Additional Tax via DRC-03

If reconciliation reveals underpaid tax or excess ITC claims from the year, pay the difference via Form DRC-03 before filing GSTR-9. Filing GSTR-9 with a known shortfall creates an irrevocable admission of tax default. Do not proceed to file until all additional liability is settled.

Compute Liabilities, Preview, Sign, and File

Click "Compute Liabilities" — the system calculates any late fee automatically if you are past December 31. You cannot file without paying the late fee. Download the draft PDF preview, verify all figures, select your authorised signatory, and file using DSC or EVC. Once filed, an ARN (Acknowledgment Reference Number) is generated and sent to your registered mobile and email. Filing is final — no revision option exists.

Outward Supply Reconciliation (GSTR-1 vs Books)

Total sales declared across all GSTR-1 filings for the year must match your revenue per books of accounts. Differences arise from missed invoices, credit notes applied in different periods, and export amendments. Every difference needs to be identified, explained, or corrected through Table 10/11 of GSTR-9.

ITC Three-Way Reconciliation (GSTR-3B vs GSTR-2B vs Books)

This is the highest-risk area.

• ITC claimed in GSTR-3B each month (what you actually claimed)
• ITC available in GSTR-2B (the legal maximum per supplier filings)
• ITC in your purchase register (all eligible invoices in your books)

Claiming ITC in GSTR-3B that exceeds GSTR-2B availability generates automatic GSTN alerts under Rule 36(4). Any excess must be reversed. The new Table 6A1 makes this three-way position visible to officers during desk reviews — so it needs to be accurate, not hidden.

IMS Review

For FY 2025-26, review every IMS transaction: accepted invoices, rejected credit notes, and pending records. Pending records after the GSTR-3B due date for April 2026 are deemed accepted — but if ITC was not claimed in GSTR-3B, it will show as an unexplained gap in Table 8D.

Tax Payment Verification (GSTR-3B vs Actual Liability)

Total tax paid across all GSTR-3B filings must match your actual annual tax liability. Any shortfall must go through DRC-03. The figures in Table 9 are locked — you cannot edit them — but you can compare them with your books and pay any difference before filing.

Skipping the IMS Dashboard Review

With Table 8A now IMS-driven, filing GSTR-9 without reviewing IMS action history means filing with an incomplete picture of your ITC position. Check every pending record before you touch the GSTR-9 form.

Leaving Tables 10–14 Blank

These tables capture amendments declared in April–November 2026 that relate to FY 2025-26. They are the most commonly omitted section. If you or your vendors made any amendments to FY 2025-26 invoices after March 31, those need to be in here.

Filing GSTR-9 Before GSTR-9C When Both Are Required

Per Circular 246/03/2025, if your turnover exceeds ₹5 crore, filing only GSTR-9 and postponing GSTR-9C means late fees continue running. File both together in the same session.

Not Verifying Aggregate Annual Turnover

Aggregate turnover includes exempt supplies, exports, and inter-state supplies — not just taxable domestic sales. Many businesses cross ₹2 crore without realising it when the full aggregate is calculated.

Assuming ITC Claimed in GSTR-3B Matches GSTR-2B

It rarely does perfectly. Even a ₹5,000 excess ITC claim against GSTR-2B creates a Rule 36(4) exposure. The new Table 6A1 makes this visible to officers — reconcile it honestly rather than hoping it goes unnoticed.