How to File GST Returns as an Ecommerce Seller in India

An ecommerce seller files the same two returns as any other registered business, GSTR-1 by the 11th and GSTR-3B by the 20th, plus two steps nobody else has to do. Marketplace sales are reported a second time in Table 14 of GSTR-1, and the TCS the operator deducted has to be accepted on the portal before it becomes usable cash.

Miss the first step and you get a mismatch notice. Miss the second and you pay GST in cash every month while your own money sits unclaimed on the same screen.

Which GST returns an ecommerce seller actually files

Three filings matter each month, and only two of them are yours.

GSTR-8 is the one that decides whether your filing goes smoothly. The operator reports your GSTIN-wise sales and the TCS it collected, and the department holds that figure against whatever you declare in GSTR-1. Amazon and Flipkart file on the 10th, which is precisely one day before your GSTR-1 is due. That is why anything filed on the 11th at 11 pm gets compared against a figure you never checked.

Registration itself is a separate question. Under Section 24(ix) of the CGST Act, a supplier of goods through an operator liable to collect TCS registers regardless of turnover, though Notification No. 34/2023-Central Tax dated 31 July 2023 exempts small sellers who supply within a single state and hold an enrolment number. Our guide to GST registration for marketplace sellers covers where you fall.

Where marketplace sales go in GSTR-1

Marketplace sales are reported twice in the same return, and the second entry is the one most sellers skip.

First, the sale itself goes in the normal place. B2C sales go into Table 5 or Table 7 by place of supply and rate. B2B sales with a customer GSTIN go into Table 4A.

Second, the same supplies are summarised again in Table 14. Table 14(a) carries an operator-wise summary of supplies on which the marketplace collects TCS under Section 52. Table 14(b) covers supplies under Section 9(5), where the operator pays the tax instead of you. Tables 14 and 15 went live on the portal from the January 2024 tax period, and amendment tables 14A and 15A followed in March 2024.

Table 14(a) does not create fresh liability. It is a declaration, GSTIN of operator by GSTIN of operator, of what has already been reported in Tables 4 to 10. Sellers who assume it is a second liability and leave it blank to avoid double tax end up with the opposite problem: a GSTR-1 that carries no trace of the operator whose GSTR-8 names them.

If you sell restaurant food, cab rides or accommodation through a platform, Section 9(5) applies and the platform pays the tax. Those supplies go in Table 14(b) and then in Table 3.1.1(ii) of GSTR-3B. Getting that wrong in the other direction, by paying tax on a supply where the operator has already paid it, is expensive to unwind.

How to file GSTR-1 for a marketplace month

1. Download the tax report or MTR file from every marketplace for the full calendar month.

2. Total taxable value by state of supply and by GST rate, before any fee deduction.

3. Match that total to your books; investigate any variance above 1% before going further.

4. Report B2B invoices in Table 4A and B2C supplies in Tables 5 and 7 by place of supply.

5. Report credit notes for returns in Table 9B, dated when the goods came back.

6. Fill Table 14(a) with the operator-wise summary of TCS-liable supplies.

7. Fill Table 14(b) only if the operator pays tax under Section 9(5) on your supplies.

8. Compare your Table 14(a) totals against the operator’s GSTR-8 figures on the portal.

9. File GSTR-1 on or before the 11th.

Step eight is optional in the sense that nothing stops you filing without it. It is not optional in the sense that a gap you find in September costs a phone call, and the same gap found by the system in the following year costs a reply to a notice.

How to file GSTR-3B after the hard lock

GSTR-3B stopped being a return you adjust. Since the July 2025 tax period, Tables 3.1 and 3.2 are auto-populated from GSTR-1, IFF and GSTR-1A, and the portal will not let you edit them. That change came through a GSTN advisory dated 7 June 2025.

The correction route is now GSTR-1A, filed for the same tax period after GSTR-1 and before GSTR-3B. Use it and the corrected figure flows into GSTR-3B. Skip it and you file a liability you know is wrong, then clean it up through DRC-03 with interest running.

1. File GSTR-1 first, since GSTR-3B now depends on it.

2. Check Table 3.1 and 3.2 against your books before doing anything else.

3. Where outward figures are wrong, file GSTR-1A for the same period, then return to GSTR-3B.

4. Review Table 4 input tax credit against GSTR-2B line by line.

5. Enter reverse charge liability in Table 3.1(d) yourself, because the portal does not fill it.

6. Pay through the electronic cash ledger after setting off the accepted TCS credit.

7. File on or before the 20th.

Input tax credit in Table 4 is the next field expected to lock. GSTN has said ITC locking follows the outward liability phase, and commentary through 2026 has pointed at various tax periods. No advisory fixing the exact period had been issued at the time of writing, so check the “What’s New” section of the GST portal before your next filing rather than trusting a date from a blog.

How to claim the TCS the marketplace deducted

TCS does not reach your cash ledger on its own. The operator collects 0.5% of the net value of taxable supplies under Section 52(1) of the CGST Act, at the rate set by Notification No. 15/2024-Central Tax dated 10 July 2024, and reports it in GSTR-8. After that, you have to go and take it.

1. Open Services, then Returns, then “TDS and TCS Credit Received” for the tax period.

2. Open the TCS table and check the operator-wise figures against your own records.

3. Accept the correct entries and reject anything that does not belong to you.

4. File the statement. There is no fee and no tax payable on it.

5. Confirm that the amount has landed in your electronic cash ledger.

6. Set it off against GST payable while filing GSTR-3B.

Net value means taxable supplies made through the operator during the month, reduced by supplies returned in the same month. Returns processed in a later month do not reduce the earlier month’s TCS, which is why apparel and footwear sellers see the TCS figure and the settlement report drift apart. That drift is normal. An unexplained drift is not, and tracking it is what marketplace payment reconciliation is for.

Sellers running for years without ever opening this screen are common. The credit accumulates, the cash ledger stays empty, and every month’s GST gets paid twice over in effect.

The IMS step that decides your input tax credit

Your input tax credit is now settled before you open GSTR-3B, not inside it. GSTR-2B is generated on the 14th and captures only what your suppliers filed by the 13th. Whatever you did, or did not do, in the Invoice Management System by then is what you get.

An invoice left unactioned in IMS is treated as accepted when GSTR-2B generates. For an ecommerce seller that matters because the marketplace charges GST on commission, fulfilment and advertising, and those invoices are usually your largest input credit. A platform that files a corrected invoice late, or files it against the wrong GSTIN of yours, shows up as a gap you can only fix in the next cycle.

Work IMS through the month rather than on the 13th. Reject wrong invoices immediately, mark disputed ones as pending, and chase the supplier while the period is still open.

GST returns when you sell from more than one state

Each GSTIN files its own GSTR-1 and GSTR-3B. A seller holding stock in four states files eight returns a month, not two, and a nil month in one state still needs a nil return in that state.

The trap is stock without registration. If your goods sit in a fulfilment centre in a state where you have no registration, the supplies made from there have no valid GSTIN to sit under, and the operator cannot collect TCS against you correctly. Adding that warehouse as an additional place of business on the right registration is a filing problem before it is a registration problem.

Aggregate turnover is computed PAN-wide across all GSTINs. Four states at ₹1.4 crore each is ₹5.6 crore for the purpose of QRMP eligibility, GSTR-9C and the late fee cap, even though no single state crossed ₹2 crore.

Should an ecommerce seller opt into QRMP

QRMP suits a seller with steady monthly tax and a small team. It suits a seller with high returns and swinging liability much less, because tax still gets paid monthly through PMT-06 while the return only gets filed quarterly.

The 22nd applies to Category X states and the 24th to Category Y, which is decided by where you are registered. A seller registered in Haryana files on the 24th while the same seller’s Karnataka GSTIN files on the 22nd, so a multi-state seller on QRMP carries two dates, not one.

The real cost of QRMP for marketplace sellers is buyer-side. If you sell B2B and skip the IFF, your customer sees no credit in GSTR-2B for two months out of three. That conversation tends to end the QRMP experiment.

Due dates, late fees and the three-year wall

The three-year wall is the one worth reading twice. There is no appeal, no condonation and no fee that reopens it. A GSTR-3B for a period whose due date passed more than three years ago simply has no submit button, and every consequence that follows from the unfiled return stays permanent.

Annual filing sits on top of this. GSTR-9 is due by 31 December following the financial year, so 31 December 2026 for FY 2025-26, and GSTR-9C applies where aggregate turnover crosses ₹5 crore under Rule 80(3) of the CGST Rules.

Why ecommerce sellers get GST notices

The notices we see cluster around four things, and none of them involve deliberate evasion.

Turnover declared in GSTR-1 falls short of the figure the operator reported in GSTR-8, usually because the seller booked settlement amounts rather than gross sales. Our guide to ecommerce accounting sets out the correct method. Table 14 sits empty for months, so the operator-wise trail does not exist. Input tax credit claimed in GSTR-3B exceeds GSTR-2B, because commission invoices were claimed from the marketplace tax invoice without checking the portal. And returns are recognised in the month the refund was paid rather than the month the goods came back, which pushes credit notes into the wrong period and leaves March overstated.

A fifth, quieter one: a GSTIN in a state where sales have stopped but the registration was never cancelled. Nil returns keep falling due, nobody files them, and three years later that GSTIN is beyond repair.

[EXPERT INPUT NEEDED: one real anonymised client scenario from Ankush Goyal. Ideal shape: a seller who came to Complylocal with a GSTR-1 versus GSTR-8 mismatch notice, what the gap was in rupees, how many tax periods it spanned, how it was reconciled, and what the TCS credit turned out to be worth once it was finally accepted on the portal. One specific number makes this the section that gets quoted.]

Need help with monthly filings across several marketplaces? Talk to Ankush’s team at Complylocal Consultants about ecommerce GST return filing.

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