A GST Compliance Checklist for E-commerce Sellers

Selling online multiplies your GST obligations in ways that catch a lot of first-time sellers off guard. If you sell through a marketplace, you’re dealing with Tax Collected at Source (TCS) that the platform deducts and remits on your behalf — and that TCS needs to be reconciled against your own returns every period, not assumed correct.

Registration is the first trip-up: e-commerce sellers generally need GST registration regardless of turnover, and if you’re storing inventory in a fulfillment warehouse in another state, that can trigger a registration requirement there too. Sellers frequently discover this only after a state has already flagged a mismatch.

Monthly filings (GSTR-1 for outward supplies, GSTR-3B for the summary return) need to be filed on schedule even in months with negligible activity — nil returns still have deadlines. Input Tax Credit reconciliation against GSTR-2B is where most real money gets lost: credit claimed that doesn’t match a supplier’s filing gets reversed, often discovered long after the fact unless it’s checked every cycle.

The practical checklist: confirm registration in every state you hold inventory, reconcile marketplace TCS monthly, match ITC against GSTR-2B before filing (not after), and keep e-invoicing compliant if your turnover crosses the applicable threshold. If any of this sounds like it’s currently being handled ad hoc rather than on a fixed monthly process, that’s usually the first sign it’s time to hand it to someone who treats it as recurring infrastructure rather than a monthly scramble.