GSTR-3B Is Locked: How E-commerce Sellers Get GSTR-1 Right the First Time

If you sell on Amazon, Flipkart or Meesho, there is one GST change you cannot ignore any more. Since the July 2025 tax period, the tax liability that GSTR-3B picks up from your GSTR-1 is locked. You cannot type over it in GSTR-3B. Whatever you report in GSTR-1 is what you pay.

Earlier, many sellers filed a rough GSTR-1 and then "fixed" the numbers in GSTR-3B. That option is gone. This guide explains what changed, where marketplace sellers usually go wrong, and how to file a GSTR-1 that is right the first time.

What exactly is locked in GSTR-3B?

GSTN announced in its advisory of 7 June 2025 that the auto-populated liability in GSTR-3B becomes non-editable from the July 2025 return period, which means the GSTR-3B filed in August 2025 onwards.

In simple words:

• The outward tax liability in Table 3 of GSTR-3B comes from your GSTR-1, IFF or GSTR-1A.
• You can no longer increase or reduce those auto-filled values inside GSTR-3B.
• If a number is wrong, the only way to correct it for the same month is GSTR-1A, filed before you file GSTR-3B.
• If you have already filed GSTR-3B, the correction goes into a later month's GSTR-1 as an amendment.

So GSTR-1 is no longer "just a statement". It now decides how much tax leaves your cash ledger.

Why marketplace sellers feel this the most

A seller with 30 offline invoices a month can check every line by hand. A marketplace seller cannot. A normal month on Amazon or Meesho can mean thousands of orders, hundreds of returns, cancellations, replacements and orders shipped to every state.

These are the mistakes we see most often in seller reports:

1. Returns are not deducted. Meesho and Flipkart give sales and returns in separate files or separate sheets. If you report only the sales file, you pay GST on goods that came back. With the GSTR-3B lock, that extra tax is paid and cannot be reduced in 3B.

2. Cancelled orders are counted as sales. Amazon's Merchant Tax Report lists cancelled shipments too. They must be removed, or your turnover goes up for no reason.

3. Wrong place of supply. Every order shipped to another state is an inter-state supply and attracts IGST. Orders inside your own state attract CGST and SGST. If the state column is read wrongly, the tax split goes wrong, and the portal will show a mismatch you cannot fix in 3B.

4. B2B orders mixed into B2C. When a business buyer gives a GSTIN on Amazon Business or Flipkart, that invoice belongs in B2B (Table 4), not in the B2C summary. Missing it also means your buyer cannot claim input tax credit.

5. Table 14 left empty. Sales made through an e-commerce operator that collects TCS under Section 52 have to be shown in Table 14 with the operator's GSTIN. Sellers often skip it because the main tables already carry the tax.

The other two GSTR-1 rules that came in 2025

Two more changes from 2025 make a careless GSTR-1 harder to file.

HSN summary split into B2B and B2C. From the May 2025 return period, Table 12 has two tabs, one for B2B and one for B2C. HSN codes are chosen from a drop-down, not typed. You need at least 4 digits if your aggregate turnover is up to ₹5 crore and at least 6 digits above that.

Table 13 documents. The count of invoices, credit notes and other documents issued in the month now has to be reported.

For a marketplace seller, both of these need clean data. Every product needs a correct HSN code, and the invoice number series from each marketplace must be counted properly.

A simple monthly routine that works

This is the routine we suggest to sellers and CAs who file for marketplace clients.

1. Download every report for the month. For Amazon, the Merchant Tax Report (B2B and B2C). For Flipkart, the GST Sales Report. For Meesho, the TCS sales file and the returns file. Do not mix months.
2. Net the returns. Taxable value for the month is sales minus returns, rate by rate and state by state.
3. Remove cancellations. Only shipped and delivered orders are supplies.
4. Check the state of every order. Compare the ship-to state with your own registration state to decide IGST or CGST plus SGST.
5. Pull out B2B invoices. Any order with a buyer GSTIN goes to Table 4 with the invoice number and date.
6. Fill Table 14 per operator. Amazon, Flipkart and Meesho each have their own GSTIN for TCS.
7. Build the HSN summary. Split it into B2B and B2C and check that totals match the main tables.
8. Compare before you upload. Check the taxable value and tax in your draft against the marketplace TCS figures for the month. A big gap means something is missing.
9. File GSTR-1 by the 11th. Monthly filers have time until the 11th of the next month.
10. Look at GSTR-3B before filing it. If the auto-filled liability looks wrong, stop. File GSTR-1A for the same month first, then file GSTR-3B.

What to do if you find a mistake after filing GSTR-1

Do not panic, and do not try to adjust the figure in GSTR-3B. It will not let you.

• GSTR-3B not filed yet: file GSTR-1A for the same month with the corrected invoices or values. The corrected liability flows into GSTR-3B.
• GSTR-3B already filed: report the correction as an amendment in the next month's GSTR-1 (for example in Table 9A for B2B invoices or Table 10 for B2C). Tax that was short paid should be paid with interest.

Also keep the three-year limit in mind. From 2025 the portal does not accept a GSTR-1 or GSTR-3B once three years have passed from its due date. Old pending returns cannot be cleaned up "some day" any more.

How GSTPilot helps

GSTPilot was built for exactly this problem. You upload the reports you already download from Amazon, Flipkart, Meesho, Myntra, JioMart and other marketplaces, and it does the routine above for you:

• deducts returns and removes cancelled orders
• reads the ship-to state and splits IGST, CGST and SGST correctly
• moves orders with a buyer GSTIN into B2B
• fills Table 14 with the right operator GSTIN
• builds the HSN summary for both B2B and B2C
• shows you every row it could not place, so you can correct it before you file

At the end you get a JSON file that uploads straight to the GST portal (it follows the format of the GST Offline Tool V3.2.4) and an Excel workbook you can check line by line.

Since GSTR-3B now follows GSTR-1 exactly, a correct GSTR-1 is the only way to pay the right tax. Try a conversion with last month's reports, or see the plans for sellers and CA firms.

Quick answers

Can I still edit GSTR-3B at all? You can still edit the input tax credit side and other tables that are not auto-filled from GSTR-1. The outward liability auto-filled from GSTR-1, IFF or GSTR-1A is locked.

Is GSTR-1A compulsory? No. It is optional. You use it only when you need to correct the current month's GSTR-1 before filing GSTR-3B.

Does this apply to quarterly (QRMP) filers? Yes. The liability from IFF and GSTR-1 for the quarter flows into the quarterly GSTR-3B in the same way.

My marketplace already collected TCS. Do I still need to report the sales? Yes. TCS is only an advance credit in your cash ledger. You still report every sale in GSTR-1 and pay tax through GSTR-3B. The TCS credit is adjusted against that tax.