GST Annual Return Filing For FY25 Enabled: New Rules, Turnover Limits, And Compliance Tips

GST Portal Opens for FY25 Annual Return Filing: Key Points and Changes to Note

The GST portal has enabled filing of the GSTR-9 annual return and GSTR-9C reconciliation statement for FY 2024-25. The GSTR-9 is an annual return that taxpayers registered under GST must file once every financial year. It provides a summary of all monthly or quarterly GST returns filed during the year, including details of outward and inward supplies, tax paid, and input tax credit claimed.

Prabhat Ranjan, Senior Director, Nexdigm told News18 that while we all have been filing GSTR 9 and 9C for quite some time now, here are a few points which need to kept in mind for completing the filing this time around.

1. Do Not Wait for Extension: File Before the Deadline

With the deadline of 31 December 2025, there is absolutely no room for complacency. While extensions have been granted in the past due to systemic issues, going by the history of the past 2-3 years, absolutely no extensions have been granted. Thus do not plan your filings by keeping any room for expected due date extensions

2. Keep in mind the turnover limits

Taxpayers having PAN based turnover below INR 2 crores are not required to file either GSTR 9 or 9C. Taxpayers having PAN based turnover above INR 2 crores but below INR 5 crores are required to file GSTR 9 only. Both GSTR 9 and 9C are applicable in case of taxpayers, having PAN based turnover above INR crores.

3. Understand the Changes Introduced in FY 2024-25

The GST portal has introduced specific modifications to the GSTR 9 and 9C forms for this financial year. These changes majorly revolve around disclosure of ITC availed in Table 6, which in turn would affect auto populated values in Table 8B. ITC availed for invoices pertaining to the previous financial year (i.e., FY 2023-24) needs to be separately disclosed. Taxpayers would be required to identify if their systems and reports are geared to present the data bifurcations called for and plan accordingly.

4. Identify Compulsory vs. Optional Fields

A critical error most businesses make is incorrectly filling optional fields. Compulsory fields include GSTIN, reporting period, turnover summaries, HSN-wise breakdown of outward supplies, and reconciliation tables. Optional fields mainly include HSN summary of purchases, expense wise bifurcation of ITC availed (Table 14 of GSTR 9C) etc. Decision needs to be made if data is supposed to disclosed in these fields and if yes how the requisite data would be populated.

5. Revisit Earlier Returns to Identify Past Challenges

Before starting FY 2024-25 returns, thoroughly review your GSTR 9 and 9C filings from previous years. Identify recurring reconciliation issues, error patterns, rejection reasons, or corrections that were needed. Understanding past problems helps you avoid repeating the same mistakes. Check if there were specific schedules or sections where you consistently faced challenges. This analysis provides valuable insights into documentation gaps, record-keeping deficiencies, or misclassification issues that you can address proactively for the current year.

6. Maintain Robust Documentation and Record-Keeping Throughout the Year

GST compliance is inherently document heavy. Maintain comprehensive records of all purchases (ITC claimed as well as not claimed), sales, exempted supplies, credit notes, debit notes, and HSN-wise segregation. Not only this, each and every number reported in the annual returns should be backed up by proper workings and clarifications. Poor documentation leads to reconciliation failures and audit queries. Strengthening your record-keeping processes proactively to avoid last minute rush for reconciliations.

7. Reconcile Monthly Returns (GSTR 1 and 3B) with financial data

GSTR 9 is built on data from your monthly filings. Before commencing the annual return, verify that all your GSTR 1 (outward supplies) and GSTR 3B (monthly GST liability) data are accurate and consistent with your internal records. Identify and rectify any discrepancies now – the time limit for the same would be the Oct 25 monthly returns.

8. Pay Special Attention to ITC Reconciliation and Blocked Credit

One of the most complex sections in GSTR 9 and 9C involves Input Tax Credit (ITC) reconciliation. Two kinds of reconciliations are required. Firstly Table 8 of GSTR 9 requires reconciliation of ITC availed during the financial year (FY 2024-25) with ITC populated in GSTR 2B generated during the concerned financial year. This year onwards, the difference in table 8 should be reduced to a minimum by virtue of changes introduced in table 6 of GSTR 9. Secondly, Table 12 of GSTR 9C requires reconciliation of ITC availed as per GSTR 9 with ITC amount appearing in books. Taxpayers face considerable difficulties here if proper journal entries are not passed during the course of the year.

10. Create a Pre-Filing Checklist and Timeline

Develop a structured checklist covering all schedules, supporting documents, reconciliation statements, and verification steps required for GSTR 9 and 9C filing. Establish a realistic timeline working backward from the 31 December deadline, allocating adequate time for data gathering, reconciliation, review, and rectifications. Include milestones for reconciling monthly data, preparing HSN breakups, reviewing ITC claims, obtaining any required audit reports, and conducting internal quality checks. This systematic approach prevents oversights, reduces errors, and ensures that filing is completed well before the deadline without unnecessary stress or rushed decisions.

GST framework has introduced significant reforms in 2025, aiming to simplify compliance for smaller taxpayers while tightening reporting and limiting laxities for larger ones.

Brijesh Gandhi, Partner, NPV & Associates LLP explained News18 key recent changes you must know:

1. Permanent Exemption for Small Taxpayers (Turnover ≤ ₹2 Crore)

Registered persons with an aggregate turnover up to ₹2 crore in a financial year are permanently exempted from filing the annual return (Form GSTR-9) from FY 2024–25 onwards, as per Notification No. 15/2025 – Central Tax dated 17 September 2025.

2. Redesigned GSTR-9 / GSTR-9C Structure (Notification 13/2025)

Notification No. 13/2025 – Central Tax (Third Amendment Rules, 2025), effective from 22 September 2025 for most provisions, revamps the formats and reporting norms for GSTR-9 and GSTR-9C.

• Table 6: Separate disclosure of ITC availed from the prior year (A1) and current year (A2).

• Rule-wise reporting of ITC reversals under Rules 37, 37A, 38, 42, 43, and Section 17(5).

• Separate reporting of deferred ITC and IGST credit on imports claimed in the current year.

• Table 9: Enhanced reconciliation between tax liability and tax paid, with clearer splits (cash vs ITC) and stricter validations.

3. GSTR-9C / Reconciliation Statement changes

• A new line for supplies where tax is payable by e-commerce operators (Section 9(5)) has been introduced.

• Revised terminology from “tax paid” to “tax payable” to emphasize obligations.

4 No change in turnover thresholds, but more stringent compliance

• The exemption threshold for GSTR-9 (₹2 crore) and the threshold for GSTR-9C (₹5 crore) remain

• But because of more detailed rules/validations, taxpayers will need stricter record keeping, and mismatches or omissions will be more readily flagged by the system.

5. Late fee for delay filling

Late Fee for GSTR-9:

A late fee of ₹100 per day under CGST and ₹100 per day under SGST, totaling ₹200 per day of delay, is applicable. This is subject to a maximum cap of 0.25% of the taxpayer’s turnover in the State or Union Territory.

Penalty for Non-Filing of GSTR-9C:

GSTR-9C: No specific late fee is prescribed under the GST law. However, failure to file GSTR-9C is treated as a general offence under Section 125 of the CGST Act, 2017, which may attract a penalty of up to ₹25,000 under CGST and ₹25,000 under