Merchant reconciliation is the process of reconciling all payment transactions processed through a merchant's payment acceptance channels — card POS terminals, online payment gateways, PayShap, RTP, eWallet, and cash — to the settlement credits received in the merchant's bank account, and further matching each settlement to the corresponding sale in the merchant's POS, e-commerce, or ERP system. In South Africa, merchant reconciliation is complicated by: multiple payment channels with different settlement cycles; net settlement (card and gateway fees deducted before settlement); different reference formats per channel; and the need to reconcile at both a store level and a consolidated entity level for multi-site retailers.

South African card merchant settlement works as follows: (1) Transactions processed through the POS or online gateway during a trading day are batched and submitted to the card acquirer at end of day. (2) The acquirer submits the batch to Visa or Mastercard, which processes interchange. (3) The acquirer nets its fees and the interchange and settles the net amount to the merchant's bank account on T+1 or T+2 (the next or second business day after transaction). (4) A settlement statement is provided by the acquirer showing: gross transactions, interchange, acquirer fees, adjustments (refunds, chargebacks), and net settlement. Merchant reconciliation matches this settlement statement to the merchant's POS daily total and the bank statement credit.

PayShap reconciliation for merchants: PayShap credits settle individually and in real time to the merchant's bank account, with no batch settlement delay or fee deduction. Each PayShap credit on the bank statement must be matched to the corresponding sale in the POS or e-commerce system using the payment reference. The reference should ideally be the order or invoice number. eWallet reconciliation for merchants: eWallet disbursements (used for refunds or promotional payouts to customers) appear as batch debits on the merchant bank account. Each disbursement must be matched to the corresponding customer return or promotion record. eWallet credits (customers paying via their eWallet) are processed similarly to card payments — through the payment gateway and settled via net batch.

Common merchant reconciliation exceptions in South Africa: (1) POS transaction count or total differs from settlement file total — typically caused by split authorisations, offline transactions, or voided authorisations not yet reversed. (2) Settlement credit differs from settlement file net total — caused by additional fee deductions, chargebacks, or errors by the acquirer. (3) PayShap credit with no matching POS sale — customer paid but order was not captured, or duplicate payment. (4) Chargeback posted to settlement that is not in the merchant system — requires immediate investigation and evidence submission within the dispute window. (5) eWallet disbursement amount differs from authorised refund amount — system error or fraud. Each exception must be investigated and resolved within the acquirer's or provider's prescribed timeframe.