The CBIC has notified a series of crucial amendments to Form GSTR-9 (Annual Return) and Form GSTR-9C (Reconciliation Statement) through GST Notification No. 13/2025 Central Tax and GST Notification No. 15/2025 Central Tax
These notifications bring clarity on applicability thresholds, revise reporting structures, and introduce system-driven validations for GSTR 9 & 9C for FY 2024-25 onwards. While the turnover limits for filing remain the same (₹2 crore for GSTR-9 and ₹5 crore for GSTR-9C), the data disclosure and reconciliation requirements have become far more detailed and transparent.
The intent is clear, which is to make annual returns not just a summary formality, but a comprehensive verification tool that links a taxpayer’s books of accounts, GSTR-2B credits, and declared liabilities.
Who Must File GSTR-9 / GSTR-9C: Thresholds & Scope
| Turnover / Category | Requirement | Remarks |
| ≤ ₹2 crore (in a financial year) | Exempt from filing GSTR-9 | Notification No. 15/2025-CT maintains this exemption. |
| > ₹2 crore | Must file GSTR-9 | Notification 13/2025-CT (22 September 2025) mandates this. |
| > ₹5 crore | Must file GSTR-9 + GSTR-9C (self-certified) | Same notification 13/2025-CT. |
Thus, the filing net remains the same as in earlier years. What changes is the degree of detail and verification expected.
Key Changes in GSTR-9 (Annual Return) from FY 2024-25 Onward
Here are the major changes introduced and their implications:
| Change Area | What’s New / Changed | Implications & Key Notes |
| ITC Reporting | Split into two new sub tables: 6A1 (credits from preceding year availed in current year) and 6A2 (credits pertaining to current year) | Helps track cross-year credits more transparently; reduces chances of misreporting |
| Liability – Table 4,5 & 17 | Liability should include details from both GSTR 1 & GSTR 1A | Taxpayers will need to consolidate data from both GSTR 1 & 1A |
| Rule-wise Reversals / Obligations | Mandatory reporting of reversals under Rule 37, 37A, 38, 42, 43, and Section 17(5) separately (not just aggregates) | Taxpayers will need detailed workings and justification for reversals |
| Deferred / Late ITC | Deferred ITC claimed (within cut-off, up to 30 Nov) and IGST credits on imports availed later must be shown separately | Requires tracking of credits availed after year end, with proper linkage to books |
| Liability vs Payment Reconciliation | Table 9 has been redesigned to reconcile liability with actual payment, distinguishing between cash and ITC payments | Greater transparency; mismatches will be more visible to the system / authorities |
| Amendments / Credit or Debit Notes | Distinct disclosure is now required for amendments (debit/credit notes) up to the statutory cut-off dates | Ensures that all adjustments are clearly tied back to original transactions |
| Auto-populated Fields / System Validations | Certain fields will now be auto-populated from GSTR-2B(instead of GSTR-2A) | This shifts the focus to reconciling one’s data with system data; mismatches are harder to override |
Implication summarized: GSTR-9 is now less about summarizing totals and more about tracing each credit, reversal, and liability linkage in a form that is system-driven and validated.
| Table No. | New Field / Item Added/ Updates | Description | Purpose / Impact |
| Table 6 (Part III – ITC Details) | A1 – ITC of preceding FY availed in current FY (excluding Rule 37/37A ITC) | Captures ITC pertaining to the previous financial year but availed in the current FY, excluding those covered under Rule 37 or 37A. | To segregate prior-year ITC adjustments from current-year claims for better clarity. |
| A2 – Net ITC of current FY (A – A1) | Represents the net ITC pertaining exclusively to the current FY after excluding prior-year credits. | Helps reconcile ITC availed strictly for the current year. | |
| Serial J – revised | Now displays the difference between ITC available (I) and Net ITC (A2). | Enhances transparency in reconciling available vs availed ITC. | |
| Serial M – clarified | Specifies ITC availed through ITC-01, ITC-02, and ITC-02A (other than GSTR-3B/TRAN). | To clearly identify transitional and other special ITC claims. | |
| Table 7 (ITC Reversal & Ineligible ITC) | A1 – Reversal as per Rule 37A | Captures ITC reversal related to non-payment by suppliers beyond the prescribed time under Rule 37A. | Enables separate disclosure for reversals under the newly inserted Rule 37A. |
| A2 – Reversal as per Rule 38 | Records ITC reversal done as per Rule 38 (Banking & financial institutions). | Ensures precise reporting for sector-specific reversals. | |
| Table 8 (Other ITC-related Information) | H1 – IGST credit on import of goods availed in next FY | New field to report IGST paid on imports in current FY but ITC availed in the subsequent FY. | Ensures clarity in reporting deferred IGST credit. |
| Revised Difference (I) | Now computed as G – (H + H1) instead of earlier formula. | Aligns the difference calculation with the introduction of new H1 field. | |
| Auto-population in Table 8B | From FY 2024-25, Table 8B auto-populates ITC data from Table 6B. | Reduces manual errors and enhances automation in ITC reconciliation. | |
| Table 9 (Part IV – Tax Paid) | Revised structure | Displays tax payable vs. paid through Cash, ITC, and difference for each tax component (IGST, CGST, SGST/UTGST, Cess, Interest, Late Fee, Penalty, Others). | Provides a clearer breakup of payments, improving traceability of tax discharge. |
| Tables 10–14 (Part V – Transactions of Next FY) | Complete restructuring from FY 2024-25 onwards | Tables 10–14 redefined to align with revised timelines and ITC flow. | Brings consistency in reporting transactions related to the next FY. |
| Table 10 – Supplies/tax increased via invoices, debit notes, amendments | Reports additions in tax liability for current FY identified in next FY. Clear Label Changes made in Table 10. This presents the liability for FY reported in subsequent FY | To track upward adjustments post-FY closure. | |
| Table 11 – Supplies/tax reduced via credit notes, amendments | Reports reductions in tax liability for current FY identified in next FY. Clear Label Changes made in Table 11. This presents the liability for FY reported in subsequent FY | To capture downward adjustments for transparency. | |
| Table 12 – ITC reversed in next FY | Records reversals of ITC for the current FY done in the next FY. Clear Label Changes made in Table 12. This presents the ITC for FY reversed in subsequent FY | Ensures proper linkage of cross-year reversals. | |
| Table 13 – ITC of current FY availed in next FY (April–Oct, filed by 30th Nov) | Captures delayed ITC availed within the extended due date. — Clear Label Changes made in Table 13, This presents the ITC for FY claimed in Subsequent FY | Provides clarity on timing of ITC claims as per latest GST law timelines. | |
| Table 14 – Differential tax paid due to Table 10 & 11 | Summarizes tax impact (increase/decrease) due to amendments reported in Tables 10 & 11. | Simplifies computation of tax differentials. | |
| Clarification | For FY 2024-25 onwards, only April–October returns filed by 30th Nov of next FY to be considered. | Aligns annual return with new statutory timelines for ITC availment and amendments. | |
| Instruction Section Updates | Revised Part V wording | Updated instructions for FY 2024-25 onwards to reflect restructured tables. | Improves comprehension and compliance accuracy. |
| Guidance on ITC reporting – Table 6A1 & Table 6H | 6A1: ITC of preceding FY availed in April–Oct of next FY. 6H: ITC reclaimed under Rule 37/37A or others. | Clarifies treatment of reclaimed and carry-forward ITC for consistency. | |
| Auto-population guidance | Several ITC tables now auto-populated from GSTR-3B and other sources. | Reduces manual data entry and improves accuracy. |
Key Changes in GSTR-9C (Reconciliation / Audit) from FY 2024-25 Onward
The GSTR-9C form, which serves as a reconciliation statement between the books of accounts and the annual return (GSTR-9), has also undergone important updates through Notification No. 13/2025-Central Tax dated 22 September 2025. These revisions aim to make annual audits more transparent and data-driven while tightening the linkage between reported figures and actual business transactions.
The form now demands a higher level of accuracy and clarity in disclosures, with several new reporting requirements and improved flexibility for settling additional liabilities.
To know more about IRIS GST Software and how it can ease your GSTR9 preparation, write to support@irisgst.com.
Key Updates at a Glance
1. Separate Disclosure for E-Commerce Supplies
A new field has been introduced for reporting supplies made through e-commerce operators under Section 9(5) of the CGST Act.
➤ This ensures that transactions routed through platforms like food delivery or ride-sharing apps are distinctly captured and not merged with regular B2C sales.
2. Reconciliation Based on ‘Tax Payable’ Instead of ‘Tax Paid’
Earlier, taxpayers reported the amount of tax actually paid; now, reconciliation must be based on tax payable, i.e., the total liability arising during the year.
➤ This change highlights pending dues or under-payments more clearly, helping tax authorities and auditors identify unpaid obligations.
3. Flexibility in Discharging Additional Liability
If any additional tax liability is identified during reconciliation, taxpayers can now discharge it either in cash or through available ITC, whereas previously only cash payment was permitted.
➤ This provides greater flexibility in cash-flow management but also calls for more robust credit validation to avoid ineligible ITC usage.
4. Strengthened Linkage Between GSTR-9 and 9C
The updated 9C pulls more data directly from the revised GSTR-9 form.
➤ Any inaccuracy in the annual return automatically reflects in the reconciliation, making it essential to maintain precision and consistency across filings.
5. Enhanced Audit Trail & Supporting Documents
The new version places higher emphasis on maintaining a detailed audit trail, taxpayers and auditors must be able to substantiate all reconciled figures with proper documentation.
➤ This aligns with the government’s goal of data transparency and reducing disputes at later stages.
Why These Changes Matter (Risks & Opportunities)
Increased Compliance Risk & Scrutiny
- Mismatches between GSTR-2B / GSTR-3B / books will be harder to hide due to system validations and auto-populated fields.
- Rule-wise reversals, deferred credit, and IGST on imports (especially availed later) will attract closer examination.
- Discrepancies may lead to notices and demands; hence supporting documentation and audit trail become critical.
Opportunities for Better Control & Governance
- The focus on granular reporting pushes businesses to strengthen internal processes, IT systems, and reconciliations.
- Early detection of mismatches means corrections can be made proactively.
- The ability to use ITC (if eligible) to pay additional liabilities gives some flexibility in cash management (subject to stringent validation).
Suggested Action Plan for Businesses & Professionals
To effectively adapt to the new regime, here are steps to consider:
- Upgrade your accounting / ERP systems
Ensure systems can tag credits, reversals, adjustments, e-commerce supplies, and split across years as required. - Maintain detailed, rule-wise ITC registers
Rather than just aggregates, keep line-level details and justification for reversals, ineligible credits, deferred credits, etc. - Tag e-commerce supplies (Sec 9(5))
In your sales / invoice system, flag which supplies fall under e-commerce operator tax responsibility, so they flow into the required disclosures. - Periodic Reconciliations
Don’t leave reconciliation to year end. Do monthly or quarterly cross-checks between GSTR-3B, GSTR-2B, books and internal register to catch mismatches early. - Strong audit working papers & documentation
Be ready to show how each figure arrived at, with support documents, cross-referencing, and explanations. - Training and awareness
Ensure in-house tax, accounting, and audit teams are familiar with the new tables, disclosures, and logic. - Mock filing & validation checks
Before final submission, run validation checks (if available) and simulate likely red flags or mismatch points.
Conclusion
The changes to GSTR-9 and GSTR-9C from FY 2024-25 are not cosmetic; they signal a step change in how the tax authority perceives annual returns: not just as compliance, but as a detailed audit tool. While small taxpayers continue to enjoy relief from filing GSTR-9 (for turnover up to ₹2 crore), those above the threshold especially above ₹5 crore must brace for greater scrutiny, more granular disclosures, and tighter alignment between books and returns.
Businesses that prepare early, strengthen internal controls, run regular reconciliations, and maintain supporting documentation will fare well under the new framework. Those that leave things to the last minute may risk notices, demands, or adverse assessments.
Do you know about IRIS GST software solution
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How does IRIS GST Software help with GSTR 9?
- One-click download of GSTR 1, 2A, 2B and 3B data
- Reports on Tables 6, 10, 11, 13, 17 and 18 helps in auto-population
- In-built audit trail at an invoice level for each entry (Invoice-wise, month-wise and section-wise bifurcation of all values)
- One-click GSTR-9 data upload for all GSTINs
- Need not wait for year-end, you can get all reports at the end of any month
- A checklist of periods for which you have fetched data from GSTN. This is available return-wise for GSTR 1, 2A and 3B
- Comparison between IRIS auto-calculated data and GSTN auto-calculated data
- Quick reports on differences between table 8 of GSTR 9 vs GSTR 2a vs GSTR 2B vs Purchase Register
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