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What is Payment gateway reconciliation?

Reviewed by CA Apurav GargLast reviewed

In short

Payment gateway reconciliation matches each prepaid order on your own website with the gateway's transaction, its settlement and the bank credit, after the gateway's fees, GST on fees, refunds and chargebacks.

What it is

When a customer pays online on your own website, the payment gateway collects the money, holds it for its settlement cycle, deducts its fees and the GST on them, and pays the balance to your bank in a batch. One bank credit can cover hundreds of orders.

Payment gateway reconciliation links every step:

  1. Order in your store, with its order ID.
  2. Transaction in the gateway's report, with the gateway's payment ID.
  3. Settlement batch, listing the transactions it covers.
  4. Bank credit, matched by the settlement's UTR (bank reference number).

What to watch

  • Fees and GST on fees: the gateway issues a tax invoice for its fees. The GST on it is input tax credit, once it is in your GSTR-2B.
  • Refunds: deducted from later settlements, so a day's settlement may be lower than that day's sales.
  • Chargebacks: a customer's bank reverses a payment. The amount is deducted unless you contest it successfully.
  • Failed or pending payments: an order your store marked paid but the gateway did not capture, or the reverse.
  • Reserves: some gateways hold back part of the settlement for a period.

Payment aggregators in India work under RBI rules that require customer money to be kept in an escrow account and settled to merchants within set timelines. Your agreement with the gateway states your settlement cycle.

Routine

Each day or week, match the gateway's settlement report with your bank statement by UTR, then match the settlement's transactions with your store's orders. Book fees, GST on fees, refunds and chargebacks against the right orders, so your SKU and channel profit is correct.

Example in rupees

A D2C brand's prepaid orders for one day:

Line Amount
Successful payments, per the gateway's transaction report ₹1,50,000
Less: gateway fees (₹3,000)
Less: GST on gateway fees (₹540)
Less: refunds processed (₹4,000)
Expected settlement ₹1,42,460
Bank credit with the settlement's UTR ₹1,37,460
Difference ₹5,000

The ₹5,000 is a chargeback on one order, deducted from the settlement. The brand books it against the order and submits proof of delivery to the gateway to contest it. The figures are illustrative.

Want help applying this to your own accounts?

We handle bookkeeping, reconciliation, GST and TDS for D2C and marketplace sellers, and can walk you through how this works in your business.

General information only, not professional advice. Rules and rates change — check the official source before you act.