If the refund portal says Annexure B and GSTR-3B do not match even though your working reconciles, do not blindly submit a different number just to clear the warning. Check the refund category, tax period, tax head, GSTR-3B Table 4/eligible ITC values, Annexure B JSON/statement mapping and any excluded/ineligible credits. Save screenshots and source files; if the warning appears inconsistent after a clean rebuild, raise a GST grievance before risking a deficiency memo.
What this means for the business owner
If the refund portal says Annexure B and GSTR-3B do not match even though your working reconciles, do not blindly submit a different number just to clear the warning. Check the refund category, tax period, tax head, GSTR-3B Table 4/eligible ITC values, Annexure B JSON/statement mapping and any excluded/ineligible credits. Save screenshots and source files; if the warning appears inconsistent after a clean rebuild, raise a GST grievance before risking a deficiency memo.
The return/application history and underlying source records should tell one consistent story before any correction, payment or clarification is submitted.
Who should use this guide
This guide is for taxpayers facing the exact fact pattern in the title. It is especially useful when the portal and your books/documents do not agree, when another person handled the original filing, or when a current application/return deadline is approaching.
Why this problem usually happens
Warnings may arise from tax-head/month mapping, JSON format, excluded credits, amended returns or portal validation rather than arithmetic in the spreadsheet.
What should be checked immediately
Do not start with a correction entry. First collect the minimum evidence needed to prove what actually happened.
| Mismatch layer | Check |
|---|---|
| Month | Correct return period mapping |
| Tax head | IGST/CGST/SGST columns |
| Table 4 | Eligible/reversed ITC used |
| Annexure B | Invoice eligibility and exclusions |
| Portal | Screenshot + grievance if reproducible |
What to do now
Rebuild one month and tax head at a time; regenerate Annexure B from source 2B/purchase data; compare to filed 3B and refund statement; preserve the exact error screenshot and grievance ticket.
Before submission, the client should receive a concise summary of the problem, the proposed tax/ITC/registration treatment, payment impact and any unresolved item. After submission, keep the ARN/order/acknowledgement and filed copy.
The 2026 legal and portal position
GST Portal requires relevant GSTR-3B returns to be filed before specified ITC refund applications and validates claim data against return information.
GST Portal workflows, notifications and due-date extensions can change. The official sources below were checked for this article on 19 August 2026; recheck them immediately before filing if the matter is time-sensitive.
A realistic hypothetical
An exporter’s Excel reconciliation ties to ₹8.4 lakh eligible ITC, but the upload warning persists because one month is mapped to IGST instead of CGST/SGST in the JSON. Fixing the mapping is different from changing the underlying claim amount.
What happens if the problem is ignored
Forcing figures can make the submitted claim internally inconsistent and increase deficiency/notice risk.
What TargoLegal checks before filing or responding
TargoLegal checks filed 3B, 2B, refund period, Annexure B source/JSON and portal validation screenshot before deciding whether data or portal support is needed.
Before filing
Documents received, missing items, reconciliation difference, legal/portal route, payment impact and client approval.
After filing
Filed copy, ARN/acknowledgement, payment proof and a short open-items list for the next period.
What to send for a first review
Refund mismatch warning? Send the screenshot and refund period.
Related questions
What should I send first?
Send the GSTIN/ARN, the exact period or application stage, and the document that shows the problem. For this topic, the most useful starting point is: Refund category/period, Filed GSTR-3B, GSTR-2B/purchase register.
Can I fix this by making an adjustment in the next return?
Not automatically. A later adjustment is appropriate only when the GST law and current portal workflow allow it and the original error has been reconciled.
Should I rely only on what the GST Portal auto-populates?
No. Portal data is essential evidence, but the taxpayer remains responsible for reconciling it with books, invoices and the applicable legal conditions.
What should I keep after the correction or filing?
Keep the filed return/form, ARN or acknowledgement, payment evidence, reconciliation working and any supplier/customer correspondence that explains the change.
When should professional review be considered?
Use professional review where the issue affects material tax or ITC, several periods, a registration notice, refund, e-invoicing, cancellation/revocation or a customer’s credit.
Official sources used
Legal and portal claims on this page use official GST Portal/GSTN, CBIC, GST Council, India Code or official IRP sources. Forum discussions were used only to understand real user questions, not as legal authority.
TargoLegal Research and Editorial Desk · Last legally reviewed: 19 August 2026. Recheck live forms, notifications, portal workflows and dates before acting.
