E-commerce · marketplace GST, sorted

GST software that untangles marketplace settlements, not just invoices.

TCS reconciliation under Section 52, multi-state GSTIN handling, settlement reports matched to your sales, and GSTR-2B reconciliation so your input credit actually adds up.

Reviewed July 2026
6 min read
CA Anil Agarwal & the TatvaBooks team

Why e-commerce sellers need different GST software

Selling on Amazon or Flipkart isn't like billing a walk-in customer — the marketplace deducts TCS, nets off commission and shipping before settling, and your GST filings have to reconcile against numbers you didn't directly control. Generic billing software wasn't built for that. Here's what an online seller's books actually need.

What e-commerce GST needs	How TatvaBooks does it
Marketplace TCS under Section 52 reconciliation	TCS deducted by Amazon, Flipkart and other marketplaces is tracked against your sales so it reconciles against GSTR-8 credit rather than sitting as a mystery gap in your bank deposits.
Multi-state GSTIN handling	If you hold GSTINs in more than one state (for a warehouse or fulfilment centre), each entity's sales, purchases and returns stay separated and GST-correct instead of mixed into one ledger.
Matching settlement reports to sales	Import your marketplace settlement file and match it line by line against the sales you've booked, so commission, shipping fees and TCS deductions are accounted for rather than netted off blindly.
GSTR-2B reconciliation for input credit	Purchases — packaging, inventory, marketplace fees with GST — are matched against your GSTR-2B so ITC mismatches are caught before you claim, not after a notice.
Returns & refunds tracking	Marketplace returns are booked as credit notes against the original sale, so revenue and GST liability adjust correctly instead of being lost in a settlement report.

Honest caveat: direct API sync with Amazon Seller Central or Flipkart isn't live yet — you import your settlement and sales files, and TatvaBooks does the reconciliation from there.

For small & growing online sellers

Whether you're a single-GSTIN seller shipping from home or running fulfilment out of two or three states, the same problem shows up: settlement reports that don't obviously map to the sales you booked. TatvaBooks is sized for sellers who need that reconciliation done properly without hiring a full-time accounts team for it.

TCS, settlements and ITC — the three things that actually go wrong

Under Section 52, marketplaces collect TCS on your sales before paying out, which has to reconcile against the GSTR-8 they file on your behalf. Settlement reports bundle commission, shipping and TCS together, which makes it easy to under- or over-report revenue if you're working off bank deposits alone. And GSTR-2B reconciliation for your purchases — packaging, inventory, platform fees — is where most input credit gets lost to simple mismatches. TatvaBooks is built to catch all three before they become a notice.

Frequently asked questions

Does TatvaBooks connect directly to Amazon or Flipkart Seller Central?

Not yet, and we want to be upfront about that. There's no live API sync with marketplace seller panels today — you export your settlement and sales reports from Seller Central or Flipkart's seller dashboard and import them into TatvaBooks. Direct API sync is on our roadmap, but until it ships, the honest answer is: import, don't assume it's automatic.

How does GST software handle TCS collected by Amazon or Flipkart?

Under Section 52, marketplaces deduct TCS (currently 0.5% under CGST+SGST or 1% IGST-equivalent) on the net value of your sales before settling your payout. TatvaBooks tracks this TCS against your sales so it reconciles with the GSTR-8 the marketplace files, which is what you'll claim as credit in your GSTR-3B.

I sell from one state but I'm registered in multiple states for fulfilment — can TatvaBooks handle that?

Yes. Each GSTIN is tracked as its own entity with its own sales, purchases and returns, so a Karnataka registration used for a Bengaluru fulfilment centre doesn't get mixed into your primary Maharashtra books. You get correct state-wise GSTR-1 and GSTR-3B workings for each registration.

How do I reconcile my GSTR-2B for input credit as an online seller?

Import your purchases — inventory, packaging, marketplace platform fees with GST charged — and TatvaBooks matches them against your GSTR-2B automatically, flagging anything that doesn't match before you claim ITC. This is one of the most common notice triggers for e-commerce sellers, so we surface mismatches early rather than at filing time.

What does GST software for e-commerce sellers cost?

Multi-state GSTIN handling, inventory and settlement import are on the Business plan at ₹599/month. If you're running a larger catalogue with more users or need payroll for a small warehouse team, Growth at ₹1,099/month adds that. No per-transaction fees on either plan.

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GST for sellers

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Who it's for

For small & medium business

TCS, settlements & GSTR-2B — reconciled

Stop reconciling marketplace settlements by hand.

Import your Amazon or Flipkart settlement report and see it matched against your sales and GSTR-2B in minutes.

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