Cooking-Induced Molecular Transformations in Foods: Matrix-Dependent Effects on Bioaccessibility, Metabolism, and Health

Cooking is a transformation of food, yet its nutritional significance cannot be reduced to nutrient retention or loss. This review examines cooking as a determinant of molecular nutritional quality, focusing on how cooking environments reshape food matrices, alter the stability and accessibility of nutrients and bioactive compounds, and promote the formation of neoformed compounds of concern. Across moist-heat, dry-heat, fat-mediated, air-frying, microwave, sous-vide, and emerging technologies, nutritional outcomes depend on interactions among matrix architecture, heat- and mass-transfer conditions, and reaction pathways and biomolecular modifications. The biological significance of cooking cannot be inferred from composition alone but should be interpreted across levels of evidence, from bioaccessibility and bioavailability to metabolite formation, microbiota-mediated transformation, and, where supported by human data, host responses. Particular emphasis is placed on compound- and matrix-specific consequences for phytochemicals, vitamins, essential minerals, toxic trace elements, proteins, lipids, and starch, together with neoformed compounds including advanced glycation end products, acrylamide, heterocyclic amines, and polycyclic aromatic hydrocarbons. Overall, no cooking method is superior across all foods. Optimal nutritional outcomes depend on matching cooking conditions to matrix properties, target nutrient classes, and the balance among digestibility, metabolite exposure, nutrient preservation, and chemical safety, thereby supporting a matrix-specific framework for precision cooking.