Negative figure in GSTR-3B

To correct this: 

1. For August 2025: You can file an amendment in GSTR-3B to match GSTR-1 by adjusting the tax liabiity. Since GSTR-1 shows a negative figure due to the amendment, ensure GTR-3B reflects this correctly. 
2. For September 2025: With increased taxable amount and reduced IGST leading to a negative IGST, you can adjust this in subsequent returns or claim a refund if eligible. 

Export with payment amended downwards next month:

• GSTR-3B Table 3.1(b) can't take a negative figure. If August's amendment reduces July's export IGST and you have no other zero-rated supplies in August, the reduction can't be adjusted in August; carry it to a later month with zero-rated supplies, or claim a refund of excess tax paid (RFD-01).

• For IGST export refunds through Customs, ensure the shipping bill and GSTR-1 Table 6A match (amended values), or the refund will be withheld.

Do not force GSTR-3B to match the negative GSTR-1 amendment. GSTR-1 is a statement; GSTR-3B is the return through which tax liability is discharged. If the August amendment reduced the export taxable value and IGST already paid in July exceeds the corrected liability, the excess is generally dealt with as a refund or adjusted against a later liability where permitted—not by reporting a negative IGST liability in September GSTR-3B.

• First reconcile the July invoice, August amendment and September figures, including whether the export was under LUT/bond or with payment of IGST. An amendment from “with payment” to “without payment” can affect both tax and refund treatment.
• Report September’s actual taxable outward supplies and tax liability in GSTR-3B; do not increase taxable value merely to offset the prior overpayment. A negative amount in GSTR-1 does not itself create a negative GSTR-3B liability.
• Check the applicable refund route and supporting records before claiming the excess IGST. The precise treatment depends on the amendment fields used and whether the excess has already been adjusted or claimed.

This reconciliation is part of the monthly export-return and tax-payment workflow. Manual matching across amended invoices, GSTR-1 and GSTR-3B is difficult; automation reduces repetitive work while professional judgment remains in control. At Jir AI, our 2,000+ AI agents and 650+ integrations streamline GST, ITR, TDS, TCS and other compliance workflows, helping reduce manual workload by up to 70%. WhatsApp us to explore automating your compliance workflow: https://wa.me/message/3HVOZ7HIY4ESC1