As the financial year 2024-25 comes to a close, one of the most critical compliance tasks for regular taxpayers is filing the annual GST return in Form GSTR-9 (and GSTR-9C where applicable). While the form looks like a simple consolidation of GSTR-1 and GSTR-3B, experience shows that small mistakes and mismatches often trigger notices, scrutiny, or even future audits.
This guide summarises key “red flags” to watch out for while preparing GSTR-9 for FY 2024-25, structured in practical checkpoints for CAs, consultants, and businesses.
1. Turnover & outward supply red flags
These issues directly impact tax liability and are often the first area of system-based scrutiny.
- Mismatch between GSTR-1, GSTR-3B, and books
Ensure that turnover reported in GSTR-1, GSTR-3B, and financial statements is fully reconciled, including unbilled revenue, year-end provisions, and amendments. - Unreported or wrongly reported credit/debit notes
Cross-check that all credit and debit notes affecting FY 2024-25 are correctly reflected in GSTR-1 and appropriately adjusted in GSTR-3B and GSTR-9. - Export/SEZ values not matching ICEGATE/SEZ records
Match zero-rated supplies with ICEGATE data and SEZ endorsement to avoid refund-related disputes or mismatches in Table 4C/4D. - Wrong B2B vs B2C classification
Review large B2C entries, high-value cash sales, and e-commerce supplies to ensure correct reporting as B2B/B2C in GSTR-1 and GSTR-9. - Wrong/missing reporting of Section 9(5) ECO supplies in Table 4G1
For e-commerce operator (ECO) transactions under section 9(5), ensure correct reporting in Table 4G1 as per portal instructions and recent FAQs.
2. ITC red flags (most sensitive area)
ITC remains the most litigated zone in GST; errors here are low-hanging fruit for departmental queries.
- Table 6A (auto from GSTR-3B) not matching books
Reconcile total ITC claimed in GSTR-3B with books, vendor ledgers, and 2B-based workings before finalising Table 6A. - Previous year ITC claimed in current year not shown in 6A1
Ensure that ITC of earlier periods availed during FY 2024-25 is properly disclosed in the specific row meant for prior-period credits. - Reversals of prior-year ITC wrongly shown in Table 7
Avoid clubbing prior-year reversals with current-year reversals; incorrect presentation may distort utilisation analysis. - Capital goods ITC wrongly clubbed with inputs
Classify ITC on capital goods separately from inputs/input services to correctly populate Tables 6B, 6C, etc., and support Rule 43 working, if applicable. - Ineligible ITC under Section 17(5) not reversed
Confirm that ITC blocked under section 17(5) (motor vehicles, personal consumption, works contracts, etc.) is fully reversed and disclosed correctly in Table 7. - Differences between books ITC vs Table 7J vs GSTR-9C (Tables 12A/12F)
For taxpayers liable to GSTR-9C, ensure that total ITC as per books, as per GSTR-9, and as per reconciliation (Tables 12A/12F) is completely aligned or properly explained.
3. Reverse charge (RCM) red flags
RCM mismatches are easily traceable from 3B and 2B and often picked up in assessments.
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- RCM paid in next FY shown in wrong year
Where RCM liability of 2024-25 is discharged in 2025-26, ensure correct disclosure under Tables 4/10–14 without distorting current-year tax liability. - Missing self-invoices for unregistered supplier RCM
Check that self-invoices and payment vouchers exist for RCM on unregistered supplies and that corresponding ITC is properly supported. - RCM tax paid but ITC not availed (or vice versa)
Reconcile RCM tax discharged in cash with corresponding ITC availed; unexplained gaps often attract queries.
4. Table 8 (GSTR-2B ITC) red flags
Table 8 is a summary control for ITC vis-à-vis GSTR-2B/2A and is heavily used in system analytics.
- ITC claimed greater than ITC as per 2B (Table 8A)
Validate that ITC claimed does not exceed eligible ITC as per 2B, after considering genuine cases such as imports and ISD credits. - Import IGST credit not matching ICEGATE
Match import IGST credits with ICEGATE and bill of entry; incorrect mapping often results in credit being flagged or kept under verification. - Wrong Rule 42/43 reversals leading to incorrect Table 8C
Check the workings of common credit reversals for exempt and taxable supplies; errors here distort closing ITC figure and can signal overclaim.
5. Tax liability & Part V red flags
Part V of GSTR-9 and related disclosures often reveal underpaid tax or unreported supplies.
- Additional tax in GSTR-9 not paid via DRC-03 (cash only)
Any additional tax liability declared in GSTR-9 must be paid through DRC-03 in cash; utilisation of credit for this purpose is not permitted. - Interest and penalty mismatch vis-à-vis books
Ensure that interest and penalty paid (through 3B/DRC-03) tally with books and GSTR-9 disclosure, especially where departmental orders exist. - Supplies of FY 2024-25 reported in next FY but not disclosed in Tables 10–14
Report all subsequent-year declarations/amendments in Tables 10–14 to give a complete picture of turnover pertaining to FY 2024-25.
6. Exempt / nil / non-GST supply red flags
Incorrect classification in this block can distort turnover and exemption ratios under Rule 42.
- Incorrect values in Table 5 (D/E/F)
Scrutinise exempt, nil-rated, and non-GST supplies to ensure they are properly separated and reconciled with financials. - Wrong reporting of non-GST purchases
Purchases that are wholly outside the scope of GST (e.g., stamp duty, certain government levies) should not be misclassified in outward supply tables.
7. GSTR-9C reconciliation red flags
For taxpayers with turnover above ₹5 crore, GSTR-9C is a key audit and scrutiny document.
- Turnover mismatch (books vs GSTR-9)
Ensure that turnover as per audited financials, GSTR-9, and GSTR-1 is fully reconciled with clear notes for differences like unbilled revenue, advances, or non-GST items. - ITC differences not explained in Table 13
Any reduction or increase in ITC between books and returns should be clearly analysed and explained in the reconciliation statement. - Stock adjustments/scrapping not reported – deemed supply risk
Sudden changes in stock, write-offs, or scrapping should be evaluated for deemed supply implications and appropriately disclosed in reconciliation workings.
8. General compliance & exemption red flags
For FY 2024-25 onwards, exemption and time-limit conditions themselves can create red-flag profiles if misunderstood.
- GSTR-9 not filed within the 3-year statutory limit
Post recent changes, several GST compliances have a three-year outer limit, and non-filing within this window can permanently bar compliance and rectification opportunities. - NIL GSTR-9 not filed for inactive GSTIN when PAN-based aggregate turnover > ₹2 crore
Where PAN-level aggregate turnover exceeds ₹2 crore, GSTR-9 becomes mandatory for all regular GSTINs under that PAN, even if a particular registration was inactive or had nil outward supplies. - Not availing exemption for turnover ≤ ₹2 crore (from FY 2024-25 onward)
Notification No. 15/2025–Central Tax exempts registered taxpayers with aggregate turnover up to ₹2 crore from filing GSTR-9 for FY 2024-25 and onwards, though voluntary filing is allowed; failure to strategically use this exemption may lead to unnecessary cost and risk of mis-reporting.
Closing checklist for FY 2024-25
Before hitting “Submit” on GSTR-9/GSTR-9C for FY 2024-25, ensure that:
- All reconciliations between GSTR-1, 3B, books, and 2B are completed and documented.
- ITC (including RCM, imports, and ISD credits) is fully aligned with Rule 36/42/43 and Section 17(5).
- Additional tax, interest, or penalty is paid via DRC-03 wherever required.
- Exemption thresholds (≤ ₹2 crore for GSTR-9 and > ₹5 crore for GSTR-9C) are correctly evaluated at PAN level.
A disciplined, red-flag–driven approach to GSTR-9 not only avoids notices but also strengthens your tax governance record in an increasingly data-analytics–driven GST regime.
FCA, CWM (AAFM-US), CBV, CIFRS, R-ID, B.COM (H), RV* (IBBI)
Practising Chartered Accountant in Delhi NCR Since 2011. He can be contacted at ankitgulgulia@gmail.com or +91-9811653975.