Plant-based foods are essential component in healthy human diets. Recently, plant-based protein-rich (PBPR) foods—made from cereals and legumes using innovative processing technologies that enhance taste, texture, and nutritional value—have been driving market growth. However, processing techniques significantly alter the biochemical composition of these foods, impacting their sensory and nutritional properties. Using ¹H NMR metabolomics, this study analyzed PBPR foods across processing techniques, revealing distinct biochemical profiles. Products classified as highly processed (made from protein concentrates or isolates) were characterized by elevated levels of propylene glycol, pyroglutamate, levulinic acid, hydroxymethylfurfural (HMF), and glucose, and lower levels of myo-inositol and asparagine. In particular, fermented products, such as tempe, were associated with high levels of amino acids, 4-aminobutyrate (2-fold higher than in whole beans), and nicotinate (12.6-fold higher). These findings highlight that processing technique is associated with distinct biochemical profiles of PBPR foods, which may have implications for health, warranting precision design and optimization of the processing of PBPR.