Do’s and Don’ts While Filing GSTR-9 & GSTR-9C for FY 2024-25

The filing season for GSTR-9 (Annual Return) and GSTR-9C (Reconciliation Statement) for FY 2024-25 has begun, and this year brings significant structural, legal and reporting-level changes that every registered taxpayer must be aware of. Whether you are a practitioner, CFO, or business owner, getting this filing right is not optional, the errors can directly trigger notices, mismatches and compliance risks under the GST law.

Below is a crisp, law-aligned, practitioner-oriented “Do & Don’t Guide” for FY 2024-25, along with the key amendments that differentiate this year from the last.

DO’s — For GSTR-9 & GSTR-9C FY 2024-25:

1. Ensure all monthly returns are filed first (Mandatory Under Law):

Under Section 44 of the CGST Act and portal rules, GSTR-9 auto-populates only after all GSTR-1, IFF/GSTR-1A and GSTR-3B of the year are filed. So File all Pending Returns before filing GSTR-9 & 9C to avoids missing data in outward supplies, tax paid, and ITC tables.

2. Use the new ITC reporting structure — especially Table 6A1:

FY 2024-25 introduces Table 6A1, which exclusively reports ITC pertaining to previous financial year FY 2023-2024 but claimed in FY 2024-25. This brings legal clarity to cross-year ITC under Section 16(4).
Misreporting here may lead to notices, as the GSTN now tracks prior-year ITC separately. Therefore, Reconcile the Carried Forward ITC before filing GSTR-9. You can make amendment, if last year you carried forward the wrongly amount and keep the reconciliation ready for future reconciliation.

3. Download and reconcile Table 8A after 30th November 2025:

Table 8A becomes static only after supplier amendments stop (30 November).

Reconcile ITC with:

• Supplier GSTR-1
• Supplier GSTR-3B
• Books of accounts
• GSTR-2B (auto-drafted)
  This ensures that ITC claimed under Section 16 meets the documentary and supplier-filing conditions.

4. Reconcile turnover and tax paid before certifying GSTR-9C:

GSTR-9C requires a legally mandated reconciliation between:

• Books (Audited Financial Statements as on 31^st March-2025)
• GSTR-9 disclosures of FY 2024-2025.
• GSTR-1 / GSTR-3B filings for FY 2024-2025.

Do Reconcile the Turnover properly, if there is mismatch appears, do make disclosures accordingly in GSTR-9 & 9C. The Mismatch in turnover or tax liability is the most common reason for scrutiny.

5. Use the enhanced HSN reporting tools:

The portal now provides auto-downloadable HSN summaries from GSTR-1/1A, which must be used for accurate reporting under Table 17 of GSTR-9.

6. File GSTR-9C on time- late fee applies until audit filing is completed:

The late fee under Section 47(2) continues till GSTR-9C is filed, not just GSTR-9.
This is frequently misunderstood, ensure you finish both filings on time.

don’ts — what to absolutely avoid this year

1. Don’t file GSTR-9/9C early without supplier reconciliations:

Filing before proper reconciliation of Turnover & ITC may cause permanent mismatches, especially in Table 8A ITC reconciliation. So Do proper reconciliation of Outward supply, Inward Supply and Reverse Charge transactions.

2. Don’t misclassify or club all ITC in Table 6A:

ITC is now split into:

• 6A1: Previous-year ITC
• 6A2: Current-year ITC
• 7 Series: Reversal & re-claim
  Misclassification leads to mismatch with GSTR-3B and may invite system-generated notices.

3. Don’t consider GSTR-1 alone sufficient for ITC eligibility:

As per Section 16(2)(aa) & Rule 37A: ITC is valid only if supplier files GSTR-3B, not just GSTR-1.

4. Don’t ignore Schedule-I “no consideration” transactions:

These must be reported in outward supplies (e.g. branch transfer, related-party supply). Not reporting them inflates reconciliation risk in GSTR-9C.

5. Don’t assume GSTR-9C liability must be paid in cash:

From FY 2024-25, additional tax liability identified during GSTR-9C reconciliation can be paid through ITC or cash—earlier cash-only restriction is removed.

**6. Don’t forget: GSTR-9 and 9C once filed cannot be revised:

GST law still does not provide revision or amendment options.

Key Amendments Applicable for FY 2024-25 (Compared to FY 2023-24)

1. Introduction of Table 6A1 – Major structural reform

• Earlier returns lacked clarity for cross-year ITC.
• Now ITC of prior years claimed in FY 2024-25 must be mandatorily disclosed.

2. New reporting requirement for e-commerce turnover in GSTR-9C

• New table added for turnover reported through ECO
• Enhances transparency where TCS filings differ from books.

3. Revised “Tax Payable vs Tax Paid” reporting in GSTR-9C (Table 9K/9Q)

• Law now requires declaration of tax payable as per GSTR-9, instead of earlier auto-populated “tax paid”.
• Ensures the audit certifies liability, not payment history.

4. Introduction of mandatory late-fee reporting table (Table 17) in GSTR-9C

• Auditor must certify late fees applicable under Section 47(2).
• Strengthens enforcement for late filers.

5. Enhanced HSN-code reporting using system-generated GSTR-1 data

• Accuracy in Table 17 of GSTR-9 becomes significantly better and legally consistent.

Conclusion

The introduction of Table 6A1, revised reconciliation norms, ECO reporting and enhanced late-fee accountability marks a major shift in how annual GST compliance will be viewed by the department.

Businesses should start reconciliation early, avoid premature filing, and ensure a law-aligned, error-free disclosure to avoid future disputes.