Introduction
The GST annual return filing for FY 2024-25 brings significant structural changes that every business owner and tax professional must understand. The Central Board of Indirect Taxes and Customs (CBIC) has introduced these amendments through Notification No. 13/2025-CT dated September 17, 2025, fundamentally changing how taxpayers report Input Tax Credit (ITC), reconcile data, and handle cross-year transactions.
This isn’t just another compliance update—these changes represent a paradigm shift from routine compliance to rigorous audit checkpoints. Let’s break down everything you need to know.
Filing Requirements and Due Date
Who Must File?
- GSTR-9: Mandatory for businesses with annual turnover above ₹2 crore
- GSTR-9C: Mandatory for businesses with annual turnover above ₹5 crore
- Due Date: December 31, 2025 (for FY 2024-25)
- Exemption: Businesses with turnover up to ₹2 crore are exempt from filing GSTR-9 (Notification No. 15/2025-CT)
Pre-requisites for Filing
CRITICAL: GSTR-9 and GSTR-9C will only be enabled on the portal if:
- All GSTR-1 (or GSTR-1A/IFF) returns for FY 2024-25 are filed
- All GSTR-3B returns for FY 2024-25 are filed
- If any return is pending, the annual return forms cannot be accessed
This ensures that auto-population of Tables 4, 5, 6, 8, and 9 happens only after the complete dataset is available.
Major Changes in GSTR-9
1. New Table 6A1: Prior Year ITC Disclosure
What’s New: A completely new row has been introduced in Table 6 to capture ITC of FY 2023-24 that was claimed in FY 2024-25.
Why This Matters:
- Previously, if you claimed last year’s ITC in the current year and it wasn’t captured in the previous year’s Table 8C or 13, there was no proper disclosure mechanism
- Now you must separately show this cross-year ITC movement
- This creates additional complexity in deriving net ITC at Table 6A2
Practical Impact: You need to maintain detailed records of:
- ITC from invoices dated FY 2023-24 but claimed in FY 2024-25
- Reason for delayed claim (vendor late filing, late receipt of goods, etc.)
2. Table 7: Enhanced ITC Reversal Tracking
Separate Reporting Requirements:
Table 7A: Temporary reversals under Rule 37 Table 7A1: Reversals under Rule 37A (supplier didn’t file GSTR-3B) Table 7A2: Reversals under Rule 38 (ITC in relation to supplies received from composition dealers)
Key Change: ITC reclaimed due to Rule 37 or 37A must be shown under Table 6H, not 6A1. This distinction is crucial for accurate reporting.
Important Clarification: The GSTN has confirmed that ITC reclaimed under Rule 37/37A is treated as ITC of the year in which it is reclaimed, not of the original invoice year.
3. Table 8 Series: The Most Complex Changes
Table 8A: Back to GSTR-2A Logic
Critical Change: For FY 2024-25, Table 8A reverts from GSTR-2B-based reporting (used in FY 2023-24) to including invoices from both FY 2024-25 and early FY 2025-26.
What Gets Included:
- All invoices dated FY 2024-25 appearing in GSTR-2B from April 2024 to October 2025
- Invoices uploaded by suppliers up to November 30, 2025
What Gets Excluded:
- FY 2023-24 invoices uploaded late in FY 2024-25
Important Advisory: File GSTR-9 only after December 1, 2025, to ensure Table 8A is complete and accurate.
Table 8A: Online vs Excel Differences
Be aware that Table 8A Online and Table 8A Excel can show different values in these scenarios:
Scenario 1 – Date Amendment:
- Original invoice in GSTR-1 for January 2025
- Supplier amends date to April 30, 2025 in May 2025
- Excel: Shows in both original and amended sections
- Online: Shows only final version
Scenario 2 – Value Amendment:
- Original invoice: ₹100 IGST (January 2025)
- Amended to: ₹120 IGST (February 2025)
- Excel: Shows both values separately
- Online: Shows only ₹120
Scenario 3 – Place of Supply Change:
- Original: Interstate (IGST)
- Amended: Intrastate (CGST+SGST)
- If amendment makes ITC ineligible, it won’t appear in Table 8A Online
Action Point: Download the Excel file and reconcile carefully with your records.
New Table 8H1: Import ITC Disclosure
New Requirement: A new line has been added specifically for import-related ITC of FY 2024-25 that is availed in FY 2025-26.
Reporting Logic:
- This ITC must also be included in Table 13
- Ensures reconciliation under Table 8I shows nil difference
- Addresses longstanding confusion about import ITC timing
Table 8C: Revised Computation Rules
Key Changes:
- Table 8C will now include only ITC entries that belong to FY 2024-25, even if they appear in GSTR-2B of April to October 2025
- Positive difference: Invoices + Debit Notes of FY 2024-25 claimed in FY 2025-26
- Negative difference: Credit Notes of FY 2024-25 claimed in FY 2025-26
- Table 8C now accepts negative values to accommodate late credit notes
Important: The ITC reported in Table 8C must be reconciled with Table 13.
4. Table 9: Enhanced Tax Payment Reporting
Two New Columns Added:
- Total Tax Paid: Sum of cash and all types of ITC used
- Difference Between Tax Payable and Paid: Any remaining tax liability that must be paid through DRC-07
Benefit: This provides clearer visibility of tax payment status and outstanding liabilities.
5. Tables 12 and 13: Mandatory Cross-Year Tracking
Table 12: ITC of FY 2024-25 that was reversed in FY 2025-26 Table 13: ITC of FY 2024-25 that was availed in FY 2025-26 (up to October 2025 GSTR-3B)
Critical Rule: If such ITC exists, reporting these details is compulsory. This is not optional.
Practical Scenario:
- Invoice dated March 31, 2025
- Reflected in GSTR-2B of April 2025
- Claimed in GSTR-3B of May 2025
- Must be reported in Table 13 of FY 2024-25 return
6. Table 17: HSN Summary Download
User-Friendly Addition: The GST portal now allows downloading a consolidated HSN/SAC summary directly from GSTR-1.
How to Use:
- Go to GSTR-1 returns
- Download “Table 12 of GSTR-1/1A HSN Details”
- Data is pre-formatted for Table 17 of GSTR-9
- Reduces manual efforts and errors
7. GSTR-1A Integration
New Feature: Starting FY 2024-25, amendments made through GSTR-1A will automatically reflect in Tables 4 and 5 of GSTR-9.
What This Means:
- Any corrections to outward supplies via GSTR-1A are now captured
- Better alignment between periodic returns and annual returns
- More accurate reporting of total turnover
8. Removal of 65% Concessional Rate
Important Deletion: The 65% concessional rate of tax checkbox has been completely removed from Tables 17 and 18 of GSTR-9.
Reason: This concession is no longer applicable, so the field has been discontinued.
Major Changes in GSTR-9C
1. Table 5O: No More Clubbing
Critical Change: Previously, several reconciliation differences could be grouped into Table 5O.
New Rule:
- Adjustments from Tables 5C to 5N must be shown separately
- Only opening unbilled revenue may still be included in Table 5O
- This increases transparency but requires more detailed working papers
2. New Table 7D1: E-commerce Supply Disclosure
Purpose: Captures e-commerce supplies taxable under Section 9(5) by suppliers where the liability is on the e-commerce operator.
Impact: Businesses supplying through e-commerce platforms must now separately identify and report such transactions.
3. New Table 17: Late Fee Reporting
Significant Addition: A dedicated table for late fee payable and late fee paid has been added to GSTR-9C.
Calculation Logic (as per Circular No. 246/03/2025-GST dated January 30, 2025):
For GSTR-9:
- Calculated from December 31, 2025, to actual filing date
- ₹100 per day per Act (total ₹200 per day for CGST + SGST)
- Maximum: 0.50% of taxpayer’s turnover
For GSTR-9C:
- Calculated from the later of:
- GSTR-9 filing date, OR
- Original due date (December 31, 2025)
- Until the date of filing GSTR-9C
Example:
- GSTR-9 filed: January 5, 2026 (5 days late)
- GSTR-9C filed: January 7, 2026
- Total late fee days: 7 days (5 + 2)
4. Tables 12B and 12C: ITC Reconciliation
Table 12B: Total ITC as per Audited Financial Statements Table 12C: Reconciles with Table 13 of GSTR-9
Purpose: Creates a clear audit trail from books of accounts to GSTR-3B claims through GSTR-9.
Best Practice: Maintain detailed ITC registers categorized by:
- Inputs
- Input services
- Capital goods
- Rule-wise reversals
- Time-wise claims (current year vs prior year)
5. Additional Liability Disclosure
New Flexibility: Additional liabilities identified during reconciliation can now be paid using ITC (previously only cash was allowed).
Disclosure: Must be shown in Table 9 or Part V for unreconciled items.
Key Points to Remember
1. No Revision Allowed
CRITICAL: Once GSTR-9 and GSTR-9C are filed, they cannot be revised.
Recommendation: File both returns together after thorough verification.
2. Vendor GSTR-3B Filing Status
New Reality: Merely ensuring vendor GSTR-1 filing is no longer sufficient.
What’s Required:
- Vendors must file GSTR-3B for ITC to be eligible (Rule 37A, introduced December 2022)
- Check vendor 3B filing status in GSTR-2A
- ITC reversed under Rule 37A can be reclaimed once vendor files GSTR-3B
- Report reclaim in Table 7A1
System Change: Most platforms now restrict GSTR-1 filing until GSTR-3B is submitted, making such reversals rarer.
3. Credit Note Timing
Common Confusion: Table 4 heading says “Transactions for the year” which creates ambiguity.
Correct Treatment:
- Credit notes issued in the next financial year (within permissible timelines) should NOT be included in the previous year’s return
- They should be disclosed in the year they are actually issued
4. Deferred ITC Ledgers
Context: After the restriction on ITC claim based on GSTR-2B reflection, many eligible ITCs may not have been claimed immediately.
Reporting Requirements:
- Table 13 of GSTR-9: Show ITC claimed from April 1 to November 30, 2025
- Table 12A of GSTR-9C: Include entire ITC as per books
- Table 12C: Should match with GSTR-9 Table 13
- Next Year: Additional disclosures in Table 6A1, 6B, and 6H of GSTR-9, and Table 12B of GSTR-9C
5. IMS Dashboard Impact
Clarification: Actions taken on the Invoice Management System (IMS) dashboard do NOT directly alter entries in GSTR-9.
How It Works:
- Accepted or deemed-accepted documents already reflect in GSTR-2B
- GSTR-2B feeds into Table 8A
- So there’s an indirect impact, but no direct changes from IMS actions
6. Spillover Transactions
Definition: Transactions that span financial years (e.g., FY 2024-25 invoices claimed in FY 2025-26).
Tracking Requirements:
- Maintain a tracker for cross-year transactions
- Report in current year’s GSTR-9 Part V
- Also report in next year’s Part II (Table 6A1, etc.)
7. Closing Balance Verification
Must-Do Reconciliation:
- Verify closing balance of cash and credit ledger
- Match with GST portal across all GSTINs
- Conduct invoice-level investigation for any variances
8. Table 8C vs Table 13: Key Differences
Common Confusion Points:
Include in Table 13 but NOT in Table 8C:
- ITC on imports
- Inward supplies liable to reverse charge
Include in Table 8C but NOT in Table 13:
- Goods/services in transit (invoiced in current FY, received in next FY)
Include in Table 13 but special handling:
- Invoices accounted in books in current FY but reflected in GSTR-2B and claimed in next FY
Best Practices and Compliance Tips
1. Pre-Filing Checklist
- [ ] All GSTR-1 and GSTR-3B for FY 2024-25 filed
- [ ] Download Table 8A Excel file after December 1, 2025
- [ ] Download HSN summary from GSTR-1
- [ ] Reconcile books with GSTR-3B (Table-wise)
- [ ] Prepare detailed ITC working papers
- [ ] Verify vendor GSTR-3B filing status
- [ ] Identify cross-year ITC movements
- [ ] Check for import ITC claimed in next year
- [ ] Review all GSTR-1A amendments
2. Monthly Reconciliation
Don’t Wait Until Year-End:
- Reconcile GSTR-1 with GSTR-3B monthly
- Track ITC claims and reversals immediately
- Maintain separate registers for different ITC categories
- Document reasons for any delayed claims
3. Documentation Strategy
Maintain These Records:
- Rule-wise ITC registers (Rule 37, 37A, 38)
- Capital goods bifurcation
- Vendor GSTR-3B status tracker
- Cross-year transaction tracker
- E-commerce platform supply details
- Import documents and ITC claim timing
4. Penalty Avoidance
Late Fee Structure:
- ₹200 per day (₹100 CGST + ₹100 SGST)
- Maximum: 0.50% of turnover
- Applies to both GSTR-9 and GSTR-9C
Pro Tip: Even if you’re not ready, file a “Nil” return by the due date if turnover is below threshold. You can always update next year’s tables for adjustments.
5. Professional Assistance
When to Seek Help:
- Turnover above ₹5 crore (GSTR-9C mandatory)
- Multiple GSTINs
- Significant cross-year ITC movements
- E-commerce operations with Section 9(5) implications
- Import-export transactions
- Prior year notices or mismatches
Common Pitfalls to Avoid
1. Ignoring GSTR-1A
Problem: Many taxpayers forget to check GSTR-1A amendments.
Solution: Always review GSTR-1A before filing annual returns. These amendments now auto-populate in Tables 4 and 5.
2. Double-Counting Reclaims
Problem: ITC reclaimed after temporary reversal gets counted twice.
Solution: Use Table 6H specifically for Rule 37/37A reclaims. Don’t include them in regular ITC tables.
3. Static Table 8A Before December 1
Problem: Filing before December 1 means incomplete Table 8A data.
Solution: Wait until after December 1, 2025, when all FY 2024-25 invoices uploaded by November 30 are reflected.
4. Assuming IMS Direct Impact
Problem: Thinking IMS actions directly change GSTR-9 entries.
Solution: Understand that IMS feeds GSTR-2B, which then populates GSTR-9. Check GSTR-2B for actual impact.
5. Rushing the Filing
Problem: Filing both returns hastily without proper verification.
Solution: Since revisions aren’t allowed, take time to verify every table. File GSTR-9 and GSTR-9C together after complete review.
Strategic Insights
1. The Shift Toward Granular Compliance
These changes signal a clear policy direction: GST annual returns are moving from routine compliance to serious audit checkpoints. The government wants:
- Greater transparency in ITC claims
- Better reconciliation between books and returns
- Clear audit trails for cross-year transactions
- Reduced scope for errors or manipulation
2. System-Driven Validations
The enhanced auto-population and mandatory cross-checks mean:
- Mismatches between GSTR-2B, GSTR-3B, and books will be flagged automatically
- Manual adjustments have less room
- Documentation requirements are higher
- Notices for discrepancies will be more common
3. Increased Workload for Professionals
For tax consultants and auditors:
- Longer reconciliation time required
- Stronger working papers needed
- More documentation to defend clients
- Higher professional liability
Timeline and Action Plan
November 2025
- File all pending GSTR-1 and GSTR-3B for FY 2024-25
- Begin preliminary reconciliation
- Identify cross-year ITC movements
- Check vendor GSTR-3B status
December 1-15, 2025
- Download Table 8A Excel after December 1
- Download HSN summary
- Complete detailed reconciliation
- Prepare working papers
- Identify and document all variances
December 16-27, 2025
- Fill GSTR-9 offline/online
- Complete GSTR-9C reconciliation
- Review all tables for accuracy
- Get professional review if needed
December 28-31, 2025
- File GSTR-9
- File GSTR-9C (if applicable)
- Download acknowledgments
- Maintain records for audit
Conclusion
The GSTR-9 and GSTR-9C changes for FY 2024-25 represent the most significant overhaul in GST annual compliance since its inception. While small businesses with turnover below ₹2 crore continue to enjoy exemption relief, medium and large taxpayers face a substantially more rigorous compliance regime.
The key to successful compliance lies in:
- Proactive monthly reconciliation rather than year-end scramble
- Detailed documentation of all ITC movements and reversals
- Understanding the interplay between Tables 6, 7, 8, 12, and 13
- Timely filing to avoid late fees
- Professional assistance for complex situations
Remember, GSTR-9 and GSTR-9C cannot be revised once filed. Take your time, verify thoroughly, and file accurately. The December 31, 2025 deadline is firm, but quality should never be sacrificed for speed.
These changes aren’t just about compliance—they’re about building a robust audit trail that can withstand scrutiny. Businesses that adapt their systems and processes now will find themselves better positioned for sustainable GST compliance in the years ahead.
Disclaimer: This blog is based on notifications, circulars, and FAQs available as of November 2025. Tax laws and interpretations may change. Always consult a qualified tax professional for specific advice related to your business situation.
