A system and method for automated incoming payment and invoice reconciliation is provided. A buyer of goods sends a remittance to the seller's financial institution. The buyer's remittances is processed to generate payment data which is supplied to a payment matching application. The payment matching application retrieves buyer information from said payment data and queries the seller for all outstanding invoices of said buyer. The payment matching application then attempts to match the received payment to one or more of the buyer's outstanding invoices. If a match is found, the payment is processed and the seller's financial institution and accounting system are automatically updated. If no match is found, the payment is flagged for further processing.