A payment processing method and system is described which involves serially processing remittance documents, e.g. financial instruments, remittances, and associated documents obtained from diverse sources, electronically scanning the financial instruments and other remittance documents, thereby converting the information contained thereon into a digital format. The digital information is passed through a series of software programs and associated hardware that read the scanned financial instruments, remittances, and other documents, and compares the information obtained with preexisting information about the payor, detects errors, and the like automatically, with minimal human intervention. It also allows the information to be corrected and passed to a check encoding machine or process which imparts desired information on said checks before they are sent to a bank for deposit.The system is a plurality of electronically interconnected machines and computer servers having unique software programs installed therein, thereby allowing the remittances, financial instruments, and other documents to be processed automatically with a minimum of human interactions.