Settlement reconciliation is the process of matching the settlement amounts received in your bank account from a payment processor, card acquirer, or PayInc (BankservAfrica) to the individual underlying payment transactions that make up each settlement. In South Africa, payments collected via card (Visa, Mastercard), PayShap, RTP, or EFT are not credited to the merchant bank account individually — they are batched and settled net of fees on a one-day or two-day settlement cycle. Settlement reconciliation identifies: which transactions are included in each settlement batch; the fee and deduction applied by the processor; the net amount received; and whether any transactions were rejected, held, or reversed in the settlement file.

South African card acquirers (Absa, FNB, Nedbank, Standard Bank, and independent acquirers) settle to merchants on a net basis: the gross transaction amounts are collected from the cardholder's bank, the acquirer deducts interchange fees, scheme fees (Visa, Mastercard), and its own margin, and the net amount is credited to the merchant's bank account. The settlement file (typically provided by the acquirer as a CSV or via API) shows gross transactions, fee line items, and the net settlement amount. Settlement reconciliation matches the net credit on the bank statement to the net settlement amount in the settlement file, and further matches each transaction in the settlement file to the corresponding order or invoice in the merchant's POS or e-commerce system.

PayShap settles individually and in real time — each PayShap payment results in an immediate credit to the merchant's bank account (there is no batch settlement delay). This means PayShap settlement reconciliation is a line-by-line match between each PayShap credit on the bank statement and the corresponding PayShap transaction in the order management system, matched by amount and the payment reference embedded in the PayShap request. Card settlement, by contrast, involves batch settlement files with multiple transactions aggregated, net fees deducted, and potential for disputes and chargebacks to affect the settlement amount. The two processes require different reconciliation workflows.

Common settlement reconciliation exceptions include: (1) Transactions in the merchant's system not appearing in the settlement file (not yet settled, pending, or held by the acquirer). (2) Settlement file transactions not matched to a merchant system order (reference mismatch, orphaned transactions). (3) Settlement amount differs from gross order amount (fees applied at incorrect rate, excess hold by acquirer). (4) Chargebacks or card disputes that reduce the settlement amount. (5) PayShap credits with unrecognised references. (6) Duplicate settlement credits (rare but requires immediate investigation). All exceptions must be resolved within the acquirer's dispute window (typically 5–30 days for card chargebacks).