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Evaluating PFPs by their composition fails to recognize that nutrients are embedded in food matrices and processing modifies their nutritional functionality, for example, the bioaccessibility and bioavailability. PFPs with equivalent chemical composition may experience the \u201cfood matrix effect\u201d: a difference in the nutritional outcome and health potential. This review presents food matrices attained after processing and their nutritional significance. It also delves into the complex kinetics of digestion conducive to nutrient release from matrices and nutrient interactions before absorption in the small intestine, and the role of microbial fermentation in the colon. Matrices of PFPs can be designed or redesigned and manufactured to be tasty, nutritious, sustainable, as special foods for vulnerable groups, innovative products from novel food sources, and to feed a healthy microbiota. 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