The subject application is directed to a system and method for the automated configuration for document input devices. A document processing device first receives a document, which is scanned to detect an indicia on one of the sheets of the document. The indicia, in the form of a barcode or watermark, are then decoded to generate job data representing a desired device configuration for processing the received document. The job data is then used to program a job processor and the document processing device outputs the document in accordance with the job data.