Best GST Software for Online Sellers: 7 Things to Check Before You Pay
The best GST software for an online seller is the one that reads your marketplace reports as downloaded, deducts returns, fills the HSN, document and e-commerce tables, and catches errors before the GST portal does. Price comes last. Score any tool on the seven checks below, with your own files, before you pay for a year.
- You can prepare GSTR-1 three ways: online on the portal, in GSTN's offline tool, or in a third-party application. Paid software is a choice, not a rule.
- The portal will not generate the GSTR-1 summary if Table 13 is empty while your sales tables have data.
- Marketplaces collect TCS at 0.5% of your net sales. Good software matches it against what they reported.
- A late GSTR-1 costs Rs 50 a day, capped at Rs 2,000 per return if your turnover is up to Rs 1.5 crore.
In this guide
Why is this choice different for an online seller?
Are you wondering why a tool that works well for a shop or a factory struggles with your books? Because your sales do not start as invoices you typed. They start as report files from Amazon, Flipkart or Meesho, each in its own layout, with returns and cancellations mixed in. GSTR-1, the monthly or quarterly return of your sales, wants that data regrouped into fixed tables. The software's real job is the regrouping. Everything else is decoration.
If you are still deciding whether to pay at all, read what a free GST tool does and does not do first. This page is for the next step: judging a product you are about to buy.
The seven checks
1. Does it read marketplace reports directly?
Upload the file exactly as you downloaded it. If the tool asks you to copy columns into its own Excel template, you are doing the conversion and paying for the privilege. Test every marketplace you sell on, not just the biggest one. The download steps are in our guides for Amazon, Flipkart and Meesho.
2. Does it handle returns and credit notes?
The portal's own guide says sales to consumers are reported net of credit and debit notes. So a returned order must reduce the State-wise total, and a return from a GST-registered buyer must appear as a credit note. Find one month with heavy returns and check that the tool's taxable value is lower than gross sales by the right amount.
3. Does it build the HSN summary and the document series?
Table 12 is the summary by HSN code, the product classification code. Table 13 lists the number ranges of the invoices and credit notes you issued. Both stop returns in practice. The portal blocks the summary when Table 13 is blank and your sales tables have data, and when the B2B tab of Table 12 is blank and you have B2B sales. It also warns if Table 12 differs from the other tables by more than 10%. Ask: does the tool fill these from my reports, or leave them to me?
4. Does it fill the e-commerce tables and match TCS?
Table 14 reports what you sold through each marketplace. The marketplace, in turn, reports the same sales in its own statement and collects TCS (tax collected at source) at 0.5% of the net value. You then accept that TCS on the portal and it lands in your cash ledger. A tool for sellers should give you Table 14 marketplace by marketplace and show where your figure and the marketplace's figure differ. See how TCS matching works.
5. Does it validate before upload?
A wrong GSTIN, a State code that does not exist, a tax amount that does not tally with the rate: the portal will reject these, usually on the evening of the due date. Software should list such errors in plain words, row by row, before it gives you a file.
6. What does it ask access to, and where does your data go?
There are two ways a tool can work. In the first, it gives you a JSON file (the data file the portal reads) and you upload it yourself. In the second, it connects to the GST portal on your behalf. Vendor guides describe that as a setting you switch on in your portal profile, called Manage API access, for a period you choose, and which you can revoke. Neither way is wrong. Just know which one you are agreeing to. Also ask where your sales data is stored, who in the company can see it, and whether you can delete it when you leave.
7. What is the true cost, add-ons included?
List the plan price, then ask about each extra: a second GSTIN, a second user, more invoices than the plan allows, GSTR-3B, the annual return, and help from a person. Add them up for twelve months. That total, not the headline, is the price.
A scoring table you can fill in
Give 2 if the tool does it fully with your own files, 1 if it does it with manual work from you, and 0 if it does not. Write your score in the last column.
| Check | What to test | Your score (0, 1 or 2) |
|---|---|---|
| 1. Reads marketplace reports | Upload last month's files unchanged, for every marketplace | ___ |
| 2. Returns and credit notes | Taxable value equals gross sales less returns | ___ |
| 3. HSN summary and document series | Tables 12 and 13 are filled without typing | ___ |
| 4. E-commerce tables and TCS | Table 14 per marketplace, and TCS compared with the portal | ___ |
| 5. Validation | Errors shown before the file is made | ___ |
| 6. Access and data | You know what it connects to and where data sits | ___ |
| 7. True yearly cost | Plan plus every add-on you will need | ___ |
| Total | Out of 14 | ___ |
A total of 12 or more is a tool you can rely on. Under 9, you will be patching gaps by hand every month.
A worked example
Say you sell on two marketplaces. October sales were Rs 5,00,000 before GST at 18%, and customers returned Rs 50,000 of it. You test a tool. It reads both reports (2), but ignores returns (0), fills Table 12 and leaves Table 13 to you (1), has no Table 14 (0), validates well (2), gives a file you upload yourself (2), and its price is clear (2). Total: 9 out of 14.
Now put rupees on the zero. With returns ignored you report Rs 5,00,000 and pay Rs 90,000. The right figure is Rs 4,50,000 and Rs 81,000. That is Rs 9,000 overpaid in one month.
And the price? Suppose the plan is listed at Rs 4,000 a year, a second GSTIN adds Rs 2,000 and a filing add-on adds Rs 3,000. These three figures are only an illustration, not any product's rates. The true cost is Rs 9,000, more than double the headline.
The mistake people usually make
They watch a demo done with the seller's sample data and buy an annual plan the same day. Demos never include a Meesho file with 200 returns. Ask for a trial, run last month's reports in the first week of the month, and compare the tool's totals with the return you already filed. If the numbers differ, ask why before you pay.
When is software not the answer?
Software prepares a return. It does not decide how much input tax credit to claim in GSTR-3B, and it does not reply to a notice. If your purchases are complicated, you hold more than one GSTIN, or a notice has come, budget for a person as well. The cost of each route is worked out in GST filing cost for online sellers.
Sources
- GSTR-1 user guide: ways to prepare the return, Tables 12 and 13 checks, B2C reported net of notes (GST portal) (checked 12 Nov 2026)
- TDS and TCS credit received: accepting TCS reported by e-commerce operators (GST portal) (checked 12 Nov 2026)
- Notification 15/2024-Central Tax: TCS rate for e-commerce operators (GST Council) (checked 12 Nov 2026)
- Notification 20/2021-Central Tax: cap on GSTR-1 late fee (GST Council) (checked 12 Nov 2026)
- GST return late fees, rate per day and caps (ClearTax, secondary) (checked 12 Nov 2026)
How AprilTax can help
AprilTax is a free GSTR-1 tool for online sellers, so you can run these seven checks on it at no cost. You upload the sales reports you download from Amazon, Flipkart or Meesho. It prepares the GSTR-1 (B2B, B2C, HSN summary, documents issued and the e-commerce tables), runs about 30 checks, matches the TCS your marketplaces reported, and gives you a JSON file that you upload on the GST portal yourself. Try the free GSTR-1 tool.
Frequently asked questions
Which GST software is best for online sellers?
Do I have to buy software to file GSTR-1?
Why does GST software need to handle returns separately?
What are Table 12 and Table 13 in GSTR-1?
What should GST software do about TCS?
Is it safe to give GST software access to my GST portal account?
How do I work out the true cost of GST software?
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