Significant Changes to GST Return Filing Rules from July 2025

The Goods and Services Tax (GST) return filing process is a crucial compliance requirement for businesses and financial professionals. Several major updates to GST return filing regulations are set to become effective from July 2025 on the official GST portal, introducing transformative changes to existing compliance solutions. This article delves into these key updates.

• Non-editable auto-populated values in GSTR-3B
• Time-barring of GST return submissions
• Launch of the e-way bill portal 2
• A new framework for resolving multi-jurisdictional GST disputes

October 29, 2025 Update: The GSTN issued an advisory urging taxpayers to submit any outstanding GST returns whose due dates were three years or more in the past and remain unfiled until the November tax period. Consequently, returns for October 2022 (monthly), July-September 2022 quarter (GSTR-1/3B Quarterly), FY 2021-22 (GSTR-4), and FY 2020-21 (GSTR-9/9C) will be blocked from filing starting December 1, 2025.

Major GST Return Filing Rule Changes Effective July 2025

GST return filing rules from July 2025 will undergo changes affecting all taxpayer categories. These revisions mandate accuracy and punctuality in GST return submissions, as failure to comply could result in GST notices and penalties.

The GST authorities previously announced the new GST return rules, with the GST Network (GSTN) recently updating the GST portal. The GSTN issued two new advisories on June 7, 2025, detailing these changes:

• Advisory regarding non-editable auto-populated liability in GSTR-3B
• Advisory regarding barring of GST Return on expiry of three years

Advisory on Non-Editable Auto-Populated Liability in GSTR-3B

From the July 2025 tax period onward, the values in Table-3 of GSTR-3B, which are automatically populated from GSTR-1 or the Invoice Furnishing Facility (IFF), will become non-editable. This implies that the GSTR-3B form for July 2025, due in August 2025, cannot be manually altered. Although this update was initially announced in January 2025, its implementation was postponed.

Until the June 2025 returns (whether monthly or quarterly), GSTR-3B could be edited despite its pre-filled values. However, starting with the July 2025 period, manual edits to outward supplies and associated taxes reported in Table 3 of the GSTR-3B summary return will not be permitted. These details are largely auto-filled from forms like GSTR-1 (for outward supply details) or IFF (for sales reporting in the first two months for quarterly filers).

GSTR-1A will gain increased importance with this new regulation. Taxpayers must utilize GSTR-1A for any corrections to outward supplies and their tax liabilities previously reported in GSTR-1 or IFF, with the exception of the recipient’s GSTIN. This mechanism enables taxpayers to amend or add tax liability details before submitting GSTR-3B for the corresponding tax period.

Advisory on Barring GST Returns After Three Years

On June 7, 2025, the GST Network released another advisory, implementing a rule that prevents the filing of GST returns more than three years after their due date. This means taxpayers will be unable to submit GST returns once three years have passed from the original due date. While the CBIC first announced this change with effect from October 1, 2023, the GSTN has now enforced this validation live on the official GST portal, starting July 2025.

A subsequent advisory issued on June 18, 2025, urged taxpayers to file all pending GST returns that would reach their three-year filing deadline by July 31, 2025. The advisory provided a list of GST returns and their respective tax periods for which filing will be blocked starting August 1, 2025:

Scope of the 3-year filing restriction

Relevant CGST Notification No. 28/2023 – Central Tax, issued on July 31, 2023, specifies the types of GST returns that must be filed before the three-year deadline from their due date expires. This new GST rule encompasses returns under CGST Sections 37 (Outward supplies), 39 (Summary return), 44 (Annual return), and 52 (Tax collection at source). These provisions apply to GSTR-1, GSTR-3B, GSTR-4, GSTR-5, GSTR-5A, GSTR-6, GSTR-7, GSTR-8 and GSTR-9.

Launch of E-Way Bill Portal 2

The National Informatics Centre (NIC) is set to launch a second e-way bill portal, https://ewaybill2.gst.gov.in/, from July 1, 2025. This initiative, announced via the GSTN's advisory dated June 16, 2025, aims to reduce reliance on a single portal and ensure near real-time data synchronization. The E-Way Bill2 portal is designed to synchronize e-way bill details with the main portal within seconds.

New Framework for Multi-Jurisdictional GST Disputes

The Central Board of Indirect Taxes and Customs (CBIC) released an important Circular, CGST Circular No. 250/07/2025-GST, on June 24, 2025. This circular designates the Principal Commissioner or Central Tax Commissioner as the reviewing authority under CGST Section 107. The Common Adjudicating Authorities (CAAs) will operate and report to the Principal Commissioner.

The same official will also hold revisional powers under CGST Section 108. Both sections concern handling appeals against demand or adjudication orders. Appeals against orders issued by CAAs will be handled by the Commissioner (Appeals) who has territorial jurisdiction over the Principal Commissioner or Commissioner of Central Tax supervising the adjudicating authority.

Previously, no formal legal framework existed for reviewing or hearing appeals against decisions made by CAAs, leaving the post-adjudication process unaddressed in earlier GST Circulars. This absence often led to jurisdictional confusion, procedural delays, and lapses in high-value investigations involving tax evasion cases.

Impact on Different Categories of Taxpayers

The advisory concerning the time-barring of GST returns filing affects all taxpayer categories. Even those who need to file nil returns but have not done so must ensure submission before the time limit expires. Tax teams need to be vigilant about the due dates for various returns to ensure timely filing and avoid such restrictions.

The advisory on the hard-locking of auto-filled GSTR-3B is being progressively implemented. Currently, sales details in GSTR-3B will be hard-locked, preventing edits. In the future, it is anticipated that Input Tax Credit (ITC) details, automatically populated from GSTR-2B, will also be hard-locked from edits in GSTR-3B. Let's explore the implications of the GSTR-3B hard-locking update for different taxpayer types:

For monthly GSTR-1 and GSTR-3B filers

Large taxpayers and those who file GST returns monthly will soon be unable to edit the auto-filled GSTR-3B. This measure ensures consistency between GSTR-1 and GSTR-3B, minimizing the need for last-minute adjustments and reducing potential revenue leakage.

However, it also requires finance teams to proactively adopt an invoice management system (IMS) to monitor real-time rejections of sales, credit notes, or debit notes by their buyers. Upon notification of a rejection, the supplier's team should verify the record and take appropriate action in GSTR-1A to nullify its impact in GSTR-3B. There is no room for errors, as correcting amendments in GSTR-1A becomes an additional, arduous process. Therefore, robust data import validations for your GST solution are now more critical than ever.

For quarterly GSTR-1 and GSTR-3B filers (QRMP)

Initially, quarterly filers of GSTR-1 and GSTR-3B under the Quarterly Return Monthly Payment (QRMP) scheme might perceive this update as complex. Nevertheless, the change will enhance data accuracy in GSTR-3B, thereby reducing the likelihood of GST notices due to discrepancies with GSTR-1. During the first and second months of a quarter, small taxpayers typically report their sales and tax liability via IFF.

In the final month of the quarter, they must report third-month sales, with other IFF details pre-filled. They can continue this process, making any necessary changes in GSTR-1A after the quarter's last month to cover corrections for that quarter. These sales details, along with corrections, will then be auto-filled into the quarterly GSTR-3B.

Regularly monitoring any rejections on the IMS will help taxpayers take timely action in GSTR-1A and mitigate data inconsistencies in GSTR-3B. This necessitates improved coordination and early error correction within the quarter to ensure accurate tax liability reporting.

This update does not affect composition taxable persons.

Immediate Action Plan for Taxpayers

Given the GSTN advisories effective from July 2025, taxpayers should implement the following immediate action plan:

1. Reconcile sales and tax liability promptly: Thoroughly review and reconcile all outward supply details in GSTR-1 and IFF for the relevant tax period against sales registers and e-invoicing data well before filing GSTR-3B to ensure accuracy.
2. Utilize GSTR-1A for corrections: Make all necessary amendments or corrections to outward supplies and tax liabilities exclusively through GSTR-1A before submitting GSTR-3B, as manual edits in GSTR-3B will no longer be permitted.
3. Strengthen internal controls: Enhance internal invoice management and reconciliation processes to prevent last-minute discrepancies, especially considering the locking of auto-populated liabilities in GSTR-3B.
4. File pending returns immediately: Address and file any outstanding or pending GST returns without delay, as returns cannot be filed after three years from their due date, starting July 2025.
5. Educate relevant staff: Inform and train tax teams and professionals about the new non-editable GSTR-3B rule and the critical importance of timely and accurate GSTR-1 and GSTR-1A filings to ensure seamless compliance.