Why Payment Gateway Sales Do Not Match Your Bank Credit

A founder sees Rs 5.90 lakh collected in the gateway and Rs 5.23 lakh in the bank, then asks the accountant to post the difference as gateway charges. That shortcut can hide refunds, chargebacks, held amounts, settlement cut-offs, and fee taxes. It can also make the sales ledger and GST working depend on a net cash number.

The Rs 1,800 shown above is tax charged by the gateway on its fee in this example. Whether it is eligible input tax credit is a separate legal and document review. It should not be silently netted against customer sales or outward tax.

1. 01

   Freeze the source window

   Export orders, invoices, credit or debit notes, gateway payments, refunds, disputes, settlement batches, fee invoices, and bank transactions using recorded cut-off times and time zones.

2. 02

   Reconcile orders to sales documents

   Classify captured, failed, cancelled, partially refunded, fully refunded, and disputed payments. Link customer collections to invoices and document genuine gaps before looking at the bank.

3. 03

   Build the gross-to-net bridge

   For each settlement batch, start with gross included collections and subtract or add every reported adjustment, fee, tax, reserve movement, and release to calculate expected net cash.

4. 04

   Tie batches to bank value dates

   Match the calculated net amount to the bank reference. Keep in-transit settlements open at period end rather than forcing them into the wrong date.

5. 05

   Post gateway costs separately

   Record the fee and tax from the supplier invoice according to the accounting and ITC review. Do not infer the tax breakdown solely from the net settlement difference.

6. 06

   Reconcile outward supplies to returns

   Use invoice and adjustment records to check GSTR-1 categories and bridge outward liability into GSTR-3B. Review auto-populated values; the taxpayer remains responsible for the filed return.

7. 07

   Carry an exception queue

   Assign duplicate captures, orphan settlements, missing fee invoices, unlinked refunds, unresolved chargebacks, held funds, and return differences to owners with dates and evidence.

• ✓A stable order or invoice key links the product, gateway, books, and return working.
• ✓Captured, refunded, disputed, failed, and held amounts use separate status codes.
• ✓Every settlement batch recalculates to the reported net amount.
• ✓Every bank credit links to a settlement batch or an open in-transit item.
• ✓Gateway fees and tax come from supplier records, not a balancing figure.
• ✓Sales and outward GST reconcile from invoices, not from net bank credits.
• ✓A preparer and reviewer sign off the exception queue each close.

Operations can resolve an amount that sits in the wrong settlement batch or a bank value-date cut-off. Professional review is appropriate when the mismatch changes the supply value or tax period, a refund or chargeback lacks the required document treatment, the gateway or marketplace may be the contracting seller, an export classification is uncertain, or fee-tax credit conditions are not supported.