GST Reconciliation for E-commerce Sellers: A Complete Guide

Marketplace settlement reconciliation and GST reconciliation are related but distinct exercises, and conflating them is where a lot of sellers get into trouble at filing time.

Settlement reconciliation asks: did the marketplace pay me the right amount for what I sold? GST reconciliation asks a different question: does the tax I’ve reported on my sales match what the marketplace reported collecting TCS on, and does the ITC I’m claiming match what shows up in my GSTR-2B?

The two documents often disagree because they’re built on different timing. Your books might recognize a sale on the order date; the marketplace’s TCS reporting follows the settlement date. Over a large enough volume, that timing gap alone can create a mismatch between your GSTR-1 output and what the marketplace’s TCS filings imply, even when nothing is actually wrong.

The practical sequence that avoids most GST-time surprises: reconcile settlements against your sales records first (catching missing payments and wrong deductions), then separately reconcile the TCS and commission-GST figures from those same settlements against your GSTR-2B. Trying to do both in one pass tends to produce false positives — discrepancies that look like GST problems but are actually just settlement timing.

A settlement report with commission, TCS, and net amount already broken out into separate fields — rather than netted into one final number — makes this second-pass GST reconciliation dramatically faster, because you’re not first re-deriving the tax components from a lump-sum figure before you can even start comparing them.