GST Portal Update 2025: New GST Return Rules You Can’t Ignore

GST Return Filing has become Essential Compliance for any finance profession or team. The GST return filing rules are changing from July 2025, which will have an impact on all sections of taxpayers. The changes demand accuracy and Punctuality in GST return filing, or else taxpayers may receive notices and face penalties.

The GST authorities had already notified the new return rules, but the GST Network (GSTN) updated the portal only recently. These changes are aimed at improving transparency, reducing manual errors, and encouraging timely compliance.

Major Changes in GST Return Filing Rules

Handling of Inadvertently Rejected Records on IMS

If a recipient wrongly rejects an invoice or credit note in the IMS but has already filed GSTR-3B, they can still avail or reverse ITC by requesting the supplier to re-report the same document (unchanged) in GSTR-1A of the same period or in the amendment table of a later GSTR-1/IFF. Once the recipient accepts the corrected document in IMS and recomputes GSTR-2B, the ITC is adjusted accordingly. For suppliers, re-reporting the same document does not increase their liability, as amendment tables only consider the difference (delta). Even if liability temporarily rises due to credit note rejection, it gets neutralized when the same is refiled.

File pending returns before the expiry of 3 years

As per the Finance Act, 2023, taxpayers will no longer be allowed to file GST returns after three years from their original due date. This applies to key returns under Sections 37, 39, 44, and 52—covering forms like GSTR-1, GSTR-3B, GSTR-4, GSTR-9, and others. The GST portal will implement this restriction starting from the July 2025 tax period, meaning returns due before August 2022 (or FY 2021-22 for annual returns) will be permanently barred from filing after August 1, 2025. Taxpayers are strongly advised to reconcile and file any pending returns immediately to avoid being locked out of the system permanently.

Refund Validation for QRMP on GST Portal

In May 2025, the GST portal introduced a system check to ensure that taxpayers can file a refund claim only after submitting all relevant returns, as per Para 6 of Circular No. 125/44/2019-GST. This means regular taxpayers must file all GSTR-1 and GSTR-3B returns due before the refund date, while composition taxpayers, non-residents, and ISDs must file GSTR-4, GSTR-5, or GSTR-6 accordingly. Initially, taxpayers under the QRMP scheme faced issues where the system didn’t recognize IFF data from the first two months (M1 and M2) of the quarter, blocking refund filing. This technical issue has now been resolved. QRMP taxpayers can now file refunds for invoices where GSTR-3B has already been filed but should avoid including invoices reported via IFF if the related GSTR-3B is still pending. Taxpayers are advised to file all applicable returns before submitting refund claims and may contact the GST Helpdesk for any support.

Auto-Populated Liability in GSTR-3B is Not Editable

The GST portal auto-fills tax liability in GSTR-3B based on data from GSTR-1, GSTR-1A, or IFF, and until now, taxpayers could manually edit these values. However, starting from the July 2025 tax period (filed in August 2025), these auto-populated values will become non-editable. To correct any mistakes in outward supplies, taxpayers must now use the new GSTR-1A form, which allows amendments for the same tax period before GSTR-3B is filed. This change ensures better accuracy and prevents mismatches in return filings. For complete guidance, taxpayers can refer to the GST advisories issued on October 17, 2024, and January 27, 2025.

The advisories are given below for reference: