4 Surprises in the FY 2024-25 GST Annual Return That Could Catch You Off Guard

Introduction: The Annual Compliance Scramble

For most businesses, the end of the calendar year signals a familiar routine: the annual scramble to prepare and file the GST annual return (GSTR-9) and reconciliation statement (GSTR-9C) before the December 31st deadline. This year, for the Financial Year 2024-25, that deadline is December 31, 2025. However, what is not familiar is the process itself. The filings for this period are fundamentally different and more complex than in any previous year.

The level of difficulty is so unusual that prominent tax bodies like the Bombay Chartered Accountants’ Society (BCAS) and the Malad Chamber of Tax Consultants (MCTC) have formally requested a three-month extension from the GST Council. They argue that taxpayers and professionals need more time to absorb the significant procedural changes and ensure data accuracy.

This isn’t just another year of routine compliance. Here are the four most impactful and surprising changes that every business and tax professional needs to understand to navigate this challenging filing season.

1. The Finish Line Moved: Key Rules Weren’t Finalized Until Filing Season

One of the most jarring surprises this year is that the requirements for the FY 2024-25 returns were “materially altered” by a series of government notifications issued throughout 2024 and even into mid-2025. The rules of the game were changing long after the game was played.

To compound the issue, crucial clarifications in the form of GSTN FAQs and system advisories were released as late as October and December 2025—right in the middle of the filing period. This late guidance forced taxpayers and professionals to “revisit reconciliations already prepared in good faith, leading to repeated reworking of data.” In its formal representation, the MCTC articulated the challenge this created:

“Several practical relaxations that were available for earlier years were withdrawn, while new granular disclosures were made mandatory, requiring taxpayers to reconstruct historical data based on parameters that were not required at the time of original transactions.”

2. Time Travel is Real: Your “Annual” Return Depends on Next Year’s Data

The GSTR-9 for FY 2024-25 is not based solely on transactions recorded up to March 31, 2025.

Counter-intuitively, your annual return for FY 2024-25 depends on data from the next financial year. The crucial auto-populated Table 8A, which summarizes the Input Tax Credit (ITC) available to you, will include invoices from FY 2024-25 that your suppliers upload in their returns for FY 2025-26 (specifically, from their April to October 2025 returns).

While the deadline for taxpayers to make their own adjustments or claim missed credits for FY 2024-25 is November 30, 2025, the official data from the GST portal is still in flux. According to guidance from tax professionals at H N A & Co LLP, Table 8A will only become static and final on December 1, 2025. This makes the effective time for final reconciliation extremely compressed and strongly suggests that businesses should only file their annual return after that date to ensure accuracy.

3. A Credit Isn’t Just a Credit: The Complex Lifecycle of ITC

Reporting Input Tax Credit has become a multi-year puzzle, especially for credits that are claimed, reversed, and then reclaimed.

For FY 2024-25, simply reporting your total ITC is no longer sufficient. The journey of each credit, particularly those that cross financial years, must be tracked with new precision. The GSTN has clarified that the reporting method for a reclaimed credit changes based on why it was reclaimed. For instance, reclaiming a credit because you finally paid a vendor after the 180-day limit (Rule 37) is reported differently than reclaiming a credit that you had temporarily reversed because the goods arrived late.

Further complicating matters is the introduction of new tables like Table 6A1. This table specifically captures ITC from the previous financial year (FY 2023-24) that was claimed in the current year (FY 2024-25), creating another layer of cross-year reporting. This increased complexity significantly raises the chances of misreporting if a business does not maintain meticulous, invoice-level records of its entire ITC journey—from claim to reversal to reclaim.

4. Honest Mistakes, Real Consequences: The Heightened Risk of Errors

The challenging new compliance environment means even diligent taxpayers are at a higher risk of making unintentional errors.

The cumulative effect of substantial amendments, late clarifications, and a completely new reconciliation logic has created a difficult and error-prone environment. Tax professional bodies are openly warning that the risk of making mistakes has increased, even for careful and well-intentioned taxpayers. These are not errors of deliberate non-compliance, but honest mistakes born from systemic complexity and transitional challenges.

The MCTC articulated this risk in its representation to the government, warning of the potential for unnecessary disputes.

“The cumulative effect of… has resulted in a compliance environment where even diligent taxpayers face a heightened risk of unintentional errors. Such errors, arising from transitional and systemic constraints rather than deliberate non-compliance, may lead to avoidable notices, disputes and litigation, which would neither serve the interests of revenue nor further the objective of ease of doing business.”

This heightened risk comes with real consequences. The penalty for late filing of GSTR-9 and 9C is applied on a tiered basis depending on aggregate annual turnover:

• Up to ₹5 crore: ₹50 per day (₹25 CGST + ₹25 SGST), capped at 0.04% of turnover.
• ₹5 crore to ₹20 crore: ₹100 per day (₹50 CGST + ₹50 SGST), capped at 0.04% of turnover.
• Above ₹20 crore: ₹200 per day (₹100 CGST + ₹100 SGST), capped at 0.50% of turnover.

Conclusion: Preparing for a New Compliance Reality

The GSTR-9 and GSTR-9C filings for FY 2024-25 are clearly not routine tasks. They represent a significant challenge due to profound and late-breaking changes to the compliance framework. For businesses and tax professionals, meticulous, regular reconciliation and a deep understanding of the new rules are no longer just best practices—they are essential requirements for avoiding costly errors and penalties.

The new landscape demands a more proactive and dynamic approach to compliance. This leads to a critical question for every business leader: In an era of increasingly dynamic tax rules, how can your business adapt its processes to ensure compliance accuracy when the goalposts can shift even after the game is over?