A comprehensive GSTR-9 and GSTR-9C preparation checklist for Chartered Accountants and businesses — covering ITC reconciliation, turnover verification, and common audit triggers for FY 2024-25.
0 of 35 items checked
High risk = Common audit trigger
Review = Needs CA attention
Routine = Standard check
Turnover Reconciliation
Reconcile GSTR-1 aggregate turnover with audited financial statements (P&L) Any difference >1% must be explained in GSTR-9C Part II
High risk
Reconcile GSTR-3B turnover with GSTR-1 — table 4 vs table 3.1 Mismatch triggers ASMT-10 scrutiny notices automatically
High risk
Confirm gross turnover includes exempt, nil-rated, and non-GST supplies All supplies count for threshold — omitting exempt supplies is a common error
High risk
Verify advances received on which tax was paid in GSTR-3B are adjusted in GSTR-9 Table 11 Advance tax not adjusted leads to double taxation in final settlement
Review
Confirm debit note and credit note values are correctly netted in turnover Net turnover after credit notes should match books
Routine
ITC Reconciliation
Reconcile ITC claimed in GSTR-3B Table 4A with GSTR-2B for each month ITC in excess of GSTR-2B is ineligible under Section 16(2)(aa)
High risk
Identify and reverse ITC on ineligible items under Section 17(5) — motor vehicles, food, club memberships, construction Unreversed blocked ITC is the most common GST audit demand
High risk
Verify ITC reversal under Rule 42/43 for inputs used in exempt supplies Proportionate reversal mandatory; formula: Exempt turnover / Total turnover × Common ITC
High risk
Check for ITC from suppliers whose GSTIN was cancelled during the year ITC from cancelled suppliers after cancellation date is invalid
High risk
Reconcile opening ITC balance with closing balance in electronic credit ledger Any unexplained difference suggests erroneous utilisation
Review
Verify IGST ITC utilised against CGST/SGST liability follows the mandatory order IGST ITC must be used first against IGST, then CGST, then SGST — wrong order is an error
Review
Confirm transitional credit (TRAN-1/TRAN-2) if any has been correctly carried forward TRAN credits must be supported by original documents
Routine
Output Tax Verification
Verify RCM (Reverse Charge) liability declared in GSTR-3B Table 3.1(d) covers all applicable services Common RCM omissions: legal services, GTA, import of services, security services
High risk
Confirm e-invoicing compliance if turnover >₹5 crore — all B2B invoices must have IRN Missing IRN on eligible invoices makes ITC invalid for buyer and attracts penalty
High risk
Check that zero-rated supplies (exports) are backed by LUT or IGST payment Export without LUT and without IGST payment is treated as taxable domestic supply
Review
Verify GST on inter-branch transfers (distinct persons) at market value Branch transfers attract GST even between own units in different states
Review
Confirm GST on employee perquisites (non-monetary benefits) has been considered Certain perquisites like club memberships, vehicles attract output GST under Schedule I
Routine
Filing Compliance
Ensure all monthly/quarterly GSTR-1 and GSTR-3B returns for the FY are filed Pending returns block GSTR-9 filing and attract late fees
High risk
Verify all late fees paid for delayed GSTR-3B filings are reflected correctly Unpaid late fees accumulate interest and may escalate to demand
High risk
Check GSTR-9 Table 6 (ITC details) matches sum of Table 4A of all monthly GSTR-3B Any difference to be explained in GSTR-9C Part V
Review
Confirm GSTR-9 Table 10/11 correctly captures supplies and ITC from April–June (next FY) relating to previous FY These adjustments must appear in GSTR-9 not in the subsequent year's returns
Review
Verify that all credit notes issued in the current year relating to previous FY are disclosed in GSTR-9 Table 10
Routine
Documentation & Governance
Maintain supplier-wise GSTR-2B vs purchase register reconciliation as supporting workpaper Officers specifically request this during audit — absence attracts adverse inference
High risk
Keep copies of LUT (Letter of Undertaking) filed for exports throughout the year LUT validity and timely renewal is required for zero-rated export benefit
Review
Retain e-way bill records for all consignments above ₹50,000 for 5 years Missing e-way bills for audited periods attract penalty under Section 129
Review
Maintain a register of all SCN/notices received and responses filed during the FY
Routine
Ensure digital signature (DSC) on GSTR-9C is of the practising CA with valid certificate
Routine
Common GSTR-9C Reconciliation Differences Explained
Turnover Differences
Timing differences — GST books record on invoice date; financials may record on delivery. Explain in Part V of GSTR-9C.
Forex differences — Export invoices in foreign currency: GST uses customs rate, books use RBI/FEDAI rate.
Non-GST income — Interest, dividends, salary income — included in P&L but not in GST turnover.
ITC Differences
Timing of GSTR-2B — Supplier filing delays push invoices to next month's GSTR-2B. ITC claimed in books but not yet in GSTR-2B must be reversed.
Blocked credits — Section 17(5) items expensed in P&L but ITC not claimed. Disclose in GSTR-9C.
Proportionate reversal — Rule 42/43 reversals affect ITC per books vs GST records.
Verify Supplier Compliance Before Filing
A key GSTR-9C requirement is confirming ITC from cancelled or non-compliant suppliers. Check supplier filing status before finalising your audit.
Taxpayers with aggregate annual turnover exceeding ₹2 crore in FY 2024-25 must file GSTR-9C — a reconciliation statement certified by a CA or CMA. Taxpayers below ₹2 crore must file GSTR-9 but are exempt from GSTR-9C filing. Note: turnover is aggregate across all GSTINs under the same PAN.
Late filing of GSTR-9 attracts ₹200 per day (₹100 CGST + ₹100 SGST) subject to a maximum of 0.25% of turnover in the respective state. For GSTR-9C, there is no separate late fee, but the same GSTR-9 late fee applies since GSTR-9C is filed together with GSTR-9.
No. GSTR-9 cannot be revised once filed. Any corrections to figures reported in GSTR-9 cannot be made. However, any differences between GSTR-9 and the audited accounts must be disclosed and explained in GSTR-9C Part V (Auditor's recommendation on additional liability).
The CA should collect: all monthly GSTR-1, GSTR-3B filed; GSTR-2B for each month; purchase register and sales register; bank statements; import-export documentation; ITC-04 for job work; e-way bill summary; SCN/notices and responses; LUT filings; and a reconciliation of GST turnover with income tax return and audited P&L.
