Top 10 Reconciliations Before Filing GSTR 9 and 9C for FY 2024-25
The finance teams have to run multiple reconciliations before filing the annual GST returns. Due to the volume and complexity of the new tables in GSTR-9/9C, finance teams can not rely on manual, spreadsheet-based processes. They should opt for automation, granular reconciliation, and timely data correction.
Key Takeaways
- List of 10 must reconciliations to be done before filing annual GST returns.
- What should be the ideal outcome from the GSTR-9 reconciliations.
- A pre-filing GSTR-9/9C checklist along with the critical timelines.
- Why accurate GSTR-9/9C filings gives businesses the strategic financial advantage.
Strategic Path to Accurate Annual GST Return Filing
The following 10 reconciliations are non-negotiable and must be completed, documented, and signed-off before the filing deadline.
| SL No | Name of the reconciliation | What to reconcile | Ideal outcome | Root cause for difference |
| 1. | Annual turnover | Audited Financial Statements (AFS) vs. GSTR-9 (Table 5A) | Zero difference | Variance greater than ₹5 Lakh. |
| 2. | Outward tax liability | Books liability vs. GSTR-3B tax paid | Liability = Tax paid | Unaccounted payments or short payment interest risk. |
| 3. | Outward supplies | GSTR-1 turnover vs. GSTR-3B turnover | Equal match | Invoices filed but liability under-reported. |
| 4. | Rate-wise tax | Separate calculations for 5%, 12%, 18%, 28% supplies | Balanced by rate | Missed Reverse Charge Mechanism (RCM) or misclassified supplies. |
| 5. | HSN-wise summary | GSTR-9 (Table 5N) vs. GSTR-9 (Table 17) | Equal match | Mismatch in HSN codes, leading to audit query on classification. |
| 6. | Inward ITC claimed | Books vs. GSTR-3B ITC claimed | Equal match | Excess or missed ITC in monthly returns. |
| 7. | ITC eligibility (GSTR-2B) | Eligible books ITC vs. GSTR-2B ITC | Full match for eligible ITC | Discrepancy means vendor non-filing (Rule 37A risk) or blocked credit claim. |
| 8. | ITC segregation | Prior FY ITC vs. current FY ITC (via Table 6A1) | Full disclosure | Large unexplained difference in the prior FY ITC category. |
| 9. | Closing balances | GST cash ledger + ITC ledger in books vs. GST portal | Exact reconciliation | Portal sync issues or unreconciled Electronic Credit/Cash Ledger (ECL). |
| 10. | Spillover & amendments | FY 23-24 claims/adjustments reported in GSTR-3B of FY 24-25 | Correctly tagged | Double-counting in GSTR-9 Table 4/5 or late amendments after 30th Nov deadline. |
Pre-Filing Checklist and Critical Timeline
The timeline for annual compliance is fast approaching. CFOs must ensure the team operates on a strict schedule, focusing efforts around the Section 16(4) and Section 37/39 deadline of 30th November.
| Deadline | Critical action steps | Risk mitigation focus |
| By 30th November 2025 (Absolute cut-off) | Claim all missed ITC for FY 24-25 via GSTR-3B (or forfeit it forever). Complete all GSTR-1 & GSTR-3B amendments. Document all Rule 37/37A ITC reversals with reasons. Segregate prior-year ITC (prepare data for the new Table 6A1). | ITC loss & penalty avoidance |
| By 1st December 2025 | Download the final GSTR-2B statement to verify Table 8A auto-population (which excludes prior-year invoices). | Data integrity check |
| By 20th December 2025 | Complete the 10 critical reconciliations (turnover, ITC, HSN, tax rate). Resolve all Table 6J, 8D, and 9 mismatches. Prepare Form DRC-03 for any additional tax liability identified. | Pre-audit readiness |
| By 31st December 2025 (Due date) | File GSTR-9. File GSTR-9C (mandatory if turnover > ₹5 Cr). Pay any additional tax via DRC-03 (if any). | Compliance closure |
Strategic Automation for Continuous Compliance
The complexity of the GSTR-9/9C changes for FY 2024-25 fundamentally demands a move from reactive year-end compliance to a model of continuous, automated reconciliation. The question is not if to automate, but how to integrate tax compliance seamlessly with core financial processes.
By adopting a comprehensive platform that incorporates AI-powered reconciliation, two-way vendor communication for issue resolution, and a continuous compliance framework, finance leaders can transform the annual return process. This shift ensures the GSTR-9/9C filing is a confirmation of compliance and an accurate financial closure, not a source of unexpected risk and financial drain.
Clear Finance Cloud is the dedicated tax module that integrates with your ERP to deliver these outcomes. Our platform provides the granular control, AI-powered accuracy, and automated workflows required for assured compliance and maximised working capital, turning complex annual filings into a strategic financial advantage.
About the Author
AJ
As a qualified Chartered Accountant with extensive expertise in accounting, finance, taxes, and audit, I specialise in simplifying complex regulations for a broader audience. Well-versed in tax laws across India and the GCC region, I have a keen interest in the evolving finance ecosystem. Passionate about learning, I enjoy engaging in conversations, exploring new cultures through travel, and unwinding with music.. Read more
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