In October 2025, the GST Network (GSTN) issued multiple advisories to enhance taxpayer compliance and portal functionality under the GST system. The Invoice Management System (IMS) advisory clarified that auto-population of Input Tax Credit (ITC) from GSTR-2B to GSTR-3B remains unchanged, even after IMS implementation. GSTR-2B will continue to generate automatically on the 14th of each month, while taxpayers can make IMS-related updates until GSTR-3B filing. From October 2025 onwards, taxpayers can keep credit notes pending and manually adjust ITC reversals to the extent availed. Another advisory announced that utilities for filing GSTR-9 and GSTR-9C for FY 2024-25 were enabled from 12 October 2025, urging taxpayers to file all monthly returns before submitting their annual returns by 31 December 2025. Separately, CBIC clarified that importers and businesses storing goods in warehouses in other States must obtain separate GST registration in each such State, as these warehouses constitute distinct places of business. Finally, new IMS updates introduced a ‘Pending’ option for credit notes, allowing greater flexibility in ITC reversal and dispute resolution. These changes collectively aim to streamline compliance, improve accuracy in ITC reporting, and enhance transparency in GST operations.
During the month of October, 2025, the following advisories have been issued so far in relation to the various compliances by GSTN:
- GSTN Advisory on IMS
- GSTN Advisory on GST Annual Returns
- GST Registration for Importers / Warehouses
- Changes and FAQs on IMS
The gist of these advisories is summarized below:
GSTN Advisory on IMS
GSTN has clarified as follows in relation to changes in GST returns filing w.e.f. 1st October, 2025
> No Change in Auto-Population of ITC
- Input Tax Credit (ITC) will continue to auto-populate from GSTR-2B to GSTR-3B without any manual intervention.
- The mechanism of auto-population remains unchanged due to the implementation of the Invoice Management System (IMS).
> GSTR-2B Generation
- GSTR-2B will continue to be generated automatically on the 14th of every month, without any manual intervention by taxpayers or based on the actions taken by the taxpayers.
- Taxpayers can take actions in IMS even after generation of GSTR-2B till filing of GSTR-3B and can regenerate GSTR-2B accordingly, if required.
> Credit Note Handling (Effective October 2025 period onward)
- Recipient taxpayers will have the option to keep a Credit Note or related document pending for a specified period.
- On acceptance of Credit Note or related document, the recipient will also have the flexibility to reduce ITC only to the extent of its availment by adjusting the reversal amount manually.
(Source: GSTN Advisory dated 09.10.2025)
GSTN Advisory on GST Annual Returns
GSTN has advised that utility for filing Form GSTR-9 and GSTR-9C for FY 2024-25 (Annual Return and Reconciliation Statement) has been enabled on the GSTN portal w.e.f. 12th October, 2025. Accordingly,
- Assessees should ensure that all returns i.e., GSTR-1 and GSTR-3B for the FY 2024-25 are filed to enable filing of GSTR 9 and GSTR 9C.
- Taxpayers who were registered as normal (regular) under the GST regime can now submit their annual summary and reconcile figures between their tax returns and audited accounts.
- All eligible filers must complete the process by December 31, 2025.
(Source: GSTN Advisory dated 12.10.2025)
GST Registration for Importers / Warehouses
- CBIC has issued a clarification on requirement of separate GST registration for Importers storing goods in Warehouses in other States.
- It is clarified that businesses whose principal place is in one State must obtain separate GST registration in another State where goods are stored and supplied from a warehouse or cold storage, even if operated by a third party, because such storage constitutes a place of business.
- Movements require valid tax invoices and e-way bills, and transfers between establishments under the same PAN are treated as supplies between distinct persons with applicable CGST/SGST or IGST based on place of supply rules.
- Cold storage services shall be taxable at the location of the property.
- Registered persons are required to maintain records, file returns, and discharge tax liabilities in the State where the warehouse operates.
- The business entity must ensure that invoicing, documentation, and tax payment are aligned with the actual place of supply and registration status.
(F. No. CBIC- 20016/75/2025-GST/1025 dated 25th September 2025)
Changes and FAQs on IMS
- GSTN has introduced ‘pending’ option for credit notes as a new facility and declaration of reversal amount in IMS on the GSTN portal.
- Accordingly, taxpayers are allowed to keep credit notes as “Pending” for one tax period.
- The IMS functionality have also been enhanced providing a flexibility to the taxpayers to modify their ITC reversal on acceptance of such credit notes thereby resolving many business disputes.
- Following new changes have been made:
- Allowing pending action for the records mentioned above in Question-1
- Option to declare the ‘Amount of ITC to be reduced’ in IMS by the recipient taxpayers for the records for which the ITC was already reversed or not availed by the taxpayers such as CNs, upward amendment of CN or downward amendment of Invoice/DN.
- Option to provide a remark by the recipient taxpayers at the time of taking reject or pending action on the records.
- FAQs may be referred to at the portal.
(Source: GSTN Advisory dated 17.10.2025)
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