GSTR-3B for Ecommerce Sellers: Which Number Goes Where

For a seller of goods on Amazon, Flipkart or Meesho, GSTR-3B needs three things: your sales and tax in Table 3.1(a), the inter-State part sold to unregistered buyers in Table 3.2, and your input tax credit in Table 4. Table 3.1.1 usually stays blank. TCS credit never goes into GSTR-3B.

Which table takes which number?

This article is only about where a marketplace seller's numbers sit. For the full form, late fee and interest, read what GSTR-3B is.

Is selling on Amazon a section 9(5) supply?

No. Section 9(5) covers certain notified services where the e-commerce operator itself pays the GST. When you sell goods through a marketplace, you remain the person who pays the tax, so your sales go to Table 3.1(a). The portal says tax in row (i) of Table 3.1.1 is paid by the operator, and row (ii) is for the supplier of such notified services. A seller of clothes, toys or phone covers leaves both rows empty.

Where does the TCS go?

Not in Table 4. TCS is cash that the marketplace has already deposited in your name, not credit on a purchase. You accept it in the TDS and TCS credit received form under Services, then Returns. The portal's manual says the accepted amount is credited to your electronic cash ledger only after that form is filed. You then use the cash while paying in Table 6.1. The steps are in how to claim TCS credit.

How to fill GSTR-3B as a marketplace seller

1. File GSTR-1 (or IFF) first. If GSTR-3B figures were saved before GSTR-1 was filed, the portal says the auto-fill does not happen.
2. Open GSTR-3B and check Table 3.1(a) against your GSTR-1 summary. The taxable value and tax should be the same.
3. Check Table 3.2. The State-wise total should equal your inter-State B2C sales.
4. Leave Table 3.1.1 blank unless you supply a service notified under section 9(5).
5. Open Table 4 and compare the credit with GSTR-2B and your purchase bills. Reverse credit that is not allowed.
6. File the TDS and TCS credit received form for the period so the TCS sits in your cash ledger.
7. On the payment page, set off the credit, use the cash balance, pay any shortfall by challan and file with EVC or DSC.

A worked example

A seller in Maharashtra files monthly. In October 2026 the net taxable sales through two marketplaces are Rs 4,00,000, all at 5%.

• Sales to buyers in other States: Rs 2,60,000, IGST Rs 13,000.
• Sales within Maharashtra: Rs 1,40,000, CGST Rs 3,500 and SGST Rs 3,500.
• Marketplace fee invoices in GSTR-2B: Rs 60,000 plus IGST of Rs 10,800.
• TCS accepted and credited to the cash ledger: Rs 2,000.

Table 3.1(a) shows taxable value Rs 4,00,000, IGST Rs 13,000, CGST Rs 3,500 and SGST Rs 3,500. Table 3.2 shows Rs 2,60,000 and Rs 13,000, split by State. Table 4 shows IGST credit of Rs 10,800. Total tax is Rs 20,000. After the credit, Rs 9,200 is payable in cash: IGST Rs 2,200, CGST Rs 3,500 and SGST Rs 3,500. With Rs 2,000 of TCS already in the cash ledger, the fresh deposit is about Rs 7,200. The cash ledger keeps money under each tax head, so match it head by head before you create the challan.

Can you still change the auto-filled figures?

Plan as if you cannot. A GSTN advisory dated 7 June 2025 said the liability filled from GSTR-1 would become non-editable from the July 2025 tax period. Another dated 5 December 2025 said the same for Table 3.2 from the November 2025 period. Both say the fix is GSTR-1A, filed for the same period before GSTR-3B. The portal's GSTR-3B FAQ page still describes the values as editable, so the two official pages do not match. We follow the advisories because they are newer.

Two more changes came in early 2026. The interest that the portal works out in Table 5.1 can be raised but not reduced, and the tax liability breakup on the payment page is now filled by the system and has to be confirmed.

What about April 2027? The GST Council, in its 57th meeting on 8 October 2026, recommended a new way to amend liability and input tax credit in returns, to apply from the return for April 2027. It is a recommendation so far. We did not find a notification or a final form on an official page.

When is it due?

Monthly filers file by the 20th of the next month. Under the QRMP scheme the quarterly GSTR-3B is due on the 22nd or the 24th of the month after the quarter, depending on your State, and tax for the first two months is paid by challan PMT-06 by the 25th of the next month.

The mistake sellers usually make

The common one is to type figures from the marketplace payment report into GSTR-3B. That report shows money settled, not invoices raised, so it will not agree with GSTR-1. The second is to add TCS to Table 4 as if it were input tax credit. The third shows up in a month of heavy returns. If credit notes are more than sales, the portal shows zero in Table 3.1 and not a negative figure. How to carry the balance should be worked out with a tax expert before filing. Our note on sales returns in GSTR-1 covers the reporting side.

Frequently asked questions

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