Start with two records
Export or review the day's gateway orders and the corresponding transactions in the receiving merchant account. Compare order reference, amount, payment time, and verified status. The gateway record describes the customer's checkout journey; the receiving account provides the financial record. Keep both available when investigating a mismatch.
Work through exceptions
Look for pending orders with a claimed payment, duplicate customer attempts, expired links, and deposits without an obvious order. Do not match two unrelated payments solely because their amounts are equal. Use the available transaction reference and time window, then investigate any remaining ambiguity. Record the decision and evidence used for each manual correction.
Close the loop
Update your internal invoice or fulfilment system only after the payment is confirmed. If a transaction needs a refund or support intervention, track that as a separate action. A short daily review helps detect integration errors before they become a larger support queue.