There has yet to be a consensus on the definition of functional foods (FF), and accordingly many institutions lack a comprehensive process for its classification. The Functional Food Center (FFC) has previously proposed a multi-step process for the development of functional food products and ways by which to bring them to market without means to classify established items. This article is advancing the previously proposed methodology with the addition of new steps. The newest steps focus on themes of transparency by the publishing of peer-reviewed articles for the functional food product as mandatory for accreditation. In doing so, this will provide greater access to information for the functional food market, as well as, acceptance and trustworthiness of functional claims. Additionally, the Functional Food Center has created a new system for categorizing functional foods. The new categorization system uses improved research on epidemiological and after market studies, and evaluates the quality of evidence for the functional food product (FFP) as A, B, or C. A classification of A denotes the completion of aftermarket research, epidemiological studies, and certification of functional food status.