GST IMS explained: accept, reject or pending, and what deemed acceptance costs you

The Invoice Management System (IMS) went live on the GST portal in October 2024 and has steadily gained consequences. If your team still treats it as optional, this is the explainer to read before the 14th.

What IMS is

Every outward invoice, debit note and credit note your supplier reports in GSTR-1, GSTR-1A or IFF appears in your IMS dashboard. For each record you can take one of three actions.

If you take no action, the record is deemed accepted when 2B is generated, around the 14th.

What changed in October 2025

GSTN’s advisory in September 2025 made two significant changes from the October 2025 tax period.

Credit notes can be kept pending. Previously a credit note from a supplier had to be accepted or rejected. Now you can keep it pending for a tax period, which matters when you dispute a credit note or have not yet reflected it in your books.

ITC reduction must be declared. When you accept a credit note (or it is deemed accepted), you must declare whether you have already reversed the ITC and by how much. The system uses this to compute the net effect in 2B.

In April 2026 GSTN added Bill of Entry records for imports to IMS and released an Excel offline tool, so bulk actions are now practical for high-volume taxpayers.

The two mistakes we see most

Deemed acceptance of someone else’s invoice. A supplier keys your GSTIN by mistake. Nobody checks IMS. On the 14th the ITC appears in your 2B, your 3B is auto-populated, and you have claimed credit you were never entitled to. The scrutiny notice arrives a year later.

Rejecting a genuine invoice because the reference looked wrong. The supplier wrote INV/0781, your books say INV-0781, a junior rejects it. The supplier has to re-report, and your ITC moves a month.

Both mistakes have the same root cause: IMS actions are being taken from a list on the portal instead of from a reconciliation against the books.

Running IMS from your reconciliation, not the other way round

The right order is: reconcile first, then let the reconciliation drive the IMS actions.

1. Match every IMS record against the purchase register using normalised references and value tolerance.
2. Matched records: accept.
3. Amount differences: pending, with a task to trace the credit note.
4. In IMS but not in books: check goods receipt. If received, book and accept. If not yours, reject.
5. Credit notes: accept with the ITC-reduction declaration computed from the books, or keep pending if disputed.
6. Submit the actions before the 14th, so 2B is generated from your decisions rather than from defaults.

This can be automated almost entirely. The accept and pending actions on matched and partially matched records are mechanical. The only decisions that need a human are rejections and disputed credit notes, and those should be a short list.

Our accounting demo shows the reconciliation step producing exactly this list of proposed IMS actions.

The calendar this creates

Two working days between supplier filing and 2B generation is not much. It is enough if the matching is done by software the moment 2B-eligible records appear, and impossible if a person is doing it in Excel for 30 clients.