The present disclosure includes a method and system for applying ink markings on a food product in such a manner to form a permanent marking thereon. The markings include text and graphics, and can include an advertisement, freshness information, traceability data, or other types of relevant information, or any combination thereof. The method preferably forms the markings on the food product while the product moves through a predetermined region of a food processing system. Preferably, the ink marking assembly is located above the food products to be marked and the products are marked while passing thereunder. The performance or characteristics of the marking device may be adjusted in response to selected characteristics of the food product, environmental conditions, processing conditions, compliance requirements, and the like, in order to optimize the marking process.