GSTR-9 for Online Sellers: Do You Really Need to File It?
You need to file GSTR-9 for FY 2025-26 only if your total sales under one PAN, across every marketplace and every State, crossed Rs 2 crore. Below that you are exempt. Even so, doing the year-end matching by 30 November 2026 is worth your time, because that is when the correction window closes.
- Turnover is counted on your PAN for all of India: Amazon, Flipkart, Meesho, your own website and offline sales, all GSTINs together.
- Up to Rs 2 crore: GSTR-9 is exempt. Above Rs 2 crore: due by 31 December 2026.
- Errors in FY 2025-26 returns can be fixed only till 30 November 2026, or till you file the annual return, whichever is earlier.
- Marketplaces collect 0.5% TCS on your net sales. It is your money, and the year-end check is where missed TCS shows up.
In this guide
How is your turnover counted when you sell on several marketplaces?
This is the question most sellers get wrong. The Rs 2 crore limit is not per marketplace, per State or per GSTIN. The law defines aggregate turnover as the value of all supplies of persons having the same PAN, computed on an all-India basis. Taxable, exempt and export sales all count. GST itself is left out.
Take a seller of kitchen goods with GSTINs in Gujarat and Maharashtra:
| Channel | Sales in FY 2025-26 (before GST) |
|---|---|
| Amazon | Rs 95,00,000 |
| Flipkart | Rs 60,00,000 |
| Meesho | Rs 40,00,000 |
| Own website | Rs 15,00,000 |
| Aggregate turnover | Rs 2,10,00,000 |
No single channel is anywhere near Rs 2 crore. Together they are Rs 2.10 crore, so GSTR-9 is compulsory. And it is filed once for each GSTIN, so this seller files two annual returns.
What about customer returns? Use the taxable value after credit notes, the same net figure you report through the year. Do not use the gross settlement figure from a payment report.
So, do you need to file?
| Your position | What applies for FY 2025-26 |
|---|---|
| PAN-wide turnover up to Rs 2 crore | GSTR-9 exempt. Filing is your choice |
| Above Rs 2 crore, up to Rs 5 crore | GSTR-9 for each GSTIN by 31 December 2026 |
| Above Rs 5 crore | GSTR-9 and GSTR-9C for each GSTIN by 31 December 2026 |
The exemption comes from Notification 15/2025-Central Tax and applies from FY 2024-25 onwards. Due dates, late fee slabs and the contents of the form are covered in our guide to who must file GSTR-9.
Why does the year-end check matter even if you are exempt?
Because an online seller's data comes from someone else. Each marketplace gives you its own report, in its own format, and you file GSTR-1 (sales) and GSTR-3B (tax payment) from them every month. Small gaps build up over twelve months. Three places to look:
- GSTR-1 against GSTR-3B. Total taxable value and tax should agree for the year. A gap means you paid too little or too much.
- Returns against marketplace reports. Sales returns and cancelled orders are the usual cause of differences.
- TCS credit. TCS is tax collected at source. The marketplace holds back 0.5% of your net taxable sales and deposits it with the government. You get it back only when you accept it on the GST portal. On Rs 2.10 crore of sales that is Rs 1,05,000 in a year.
The department's systems compare the same figures. It is better that you find the gap first.
What is the 30 November window?
For any financial year, mistakes in GSTR-1 and GSTR-3B can be corrected in a later month's return, but only until 30 November after the year ends, or until you file the annual return, whichever comes first. The same date is the last day to claim input tax credit on FY 2025-26 purchase invoices.
For FY 2025-26 that date is 30 November 2026. Notice the order: if you file GSTR-9 on 20 November, your window shuts on 20 November. So reconcile first, correct through your October return (filed in November), and only then file the annual return.
After 30 November, a missed sale can still be reported and paid for with interest through Form DRC-03, but missed credit is gone. Is voluntary filing worth it then? For an exempt seller the return itself adds little. The matching you do for it is what protects you.
What should you gather?
- GST sales and returns reports from each marketplace for April 2025 to March 2026. See how to download them from Amazon, Flipkart and Meesho.
- Filed GSTR-1 and GSTR-3B for all twelve months, for every GSTIN.
- The TCS your marketplaces reported and what you accepted on the portal. Our TCS guide explains where to find it.
- Purchase invoices and your GSTR-2B statements, to check input tax credit.
- Sales from your own website or offline, and any credit notes issued.
- Your electronic cash and credit ledger balances as on 31 March 2026.
The mistake sellers usually make
They look at one marketplace dashboard, see Rs 80 lakh or Rs 1 crore, and decide the annual return does not apply. Then a second channel and a second State push the PAN past Rs 2 crore without anyone adding it up.
What does that cost? The late fee is Rs 50 a day for each GSTIN when turnover is up to Rs 5 crore. Our seller with two GSTINs who files 60 days late pays 60 x Rs 50 x 2 = Rs 6,000. The fee is the smaller problem. The larger one is a year of unmatched returns with the correction window already closed.
Add up your turnover across all channels today. If it is close to Rs 2 crore, treat the return as compulsory and start now.
Sources
- CGST Act, section 2(6): aggregate turnover (CBIC) (checked 12 Nov 2026)
- CGST Act, section 44: annual return (CBIC) (checked 12 Nov 2026)
- CGST Act, section 37(3): correcting GSTR-1 (CBIC) (checked 12 Nov 2026)
- CGST Act, section 39(9): correcting GSTR-3B (CBIC) (checked 12 Nov 2026)
- CGST Act, section 16(4): time limit for input tax credit (CBIC) (checked 12 Nov 2026)
- Notification 15/2025-Central Tax: exemption up to Rs 2 crore (copy of the notification text) (checked 12 Nov 2026)
- Notification 07/2023-Central Tax: reduced late fee for GSTR-9 (GST Council) (checked 12 Nov 2026)
- Notification 15/2024-Central Tax: TCS rate for e-commerce operators (GST Council) (checked 12 Nov 2026)
How AprilTax can help
The free AprilTax GSTR-1 tool reads your Amazon, Flipkart and Meesho reports and matches the TCS your marketplaces reported, which makes the year-end check much shorter. If you want the annual return done for you, a Tax Expert files GSTR-9 online for a fixed Rs 1,499. See the Tax Expert services page.
Frequently asked questions
Do Amazon, Flipkart and Meesho sellers have to file GSTR-9?
Is the Rs 2 crore limit counted for each marketplace separately?
I have GSTINs in two States. Do I file one GSTR-9 or two?
What is the 30 November deadline for FY 2025-26?
Should I file GSTR-9 voluntarily if my turnover is below Rs 2 crore?
What rate of TCS do marketplaces collect under GST?
Do sales returns reduce my turnover for the Rs 2 crore limit?
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