The nutrition transition, characterized by a shift from traditional diets to modern dietary patterns with high-energy density and reduced nutrient diversity, is closely linked to the prevalence of acquired metabolic syndromes. The human diet comprises a complex array of both nutrient and non-nutrient components, which serve as fundamental substrates for various metabolic pathways at the cellular level. Additionally, these dietary constituents and their metabolites play a crucial role in modulating gene expression and regulating diverse cellular functions through intricate molecular mechanisms. While certain dietary components exert beneficial effects, others may have cytotoxic or adverse metabolic consequences. Recent studies highlight that metabolic activity is influenced by multiple factors, including extrinsic determinants (e.g., dietary composition, environmental exposure, xenobiotics) and intrinsic determinants (e.g., sex, age, genetic polymorphisms). Furthermore, interactions between the host and gut microbiota significantly modulate metabolic processes, impacting susceptibility to acquired metabolic disorders. Emerging evidence underscores the importance of consuming low-energy, nutrient-dense diets in promoting and maintaining optimal physiological health. In developing nations, plant-based foods constitute a predominant portion of the diet, largely due to the limited consumption of animal-derived products, which is constrained by economic factors and cultural or religious practices. However, reliance on plant-based diets is frequently associated with micronutrient deficiencies and suboptimal bioavailability of essential nutrients. Several dietary factors influence nutrient assimilation, including the food matrix composition, nutrient interactions, and the presence of anti-nutritional compounds such as polyphenols, phytates, dietary fiber, oxalates, proteins, lipids, and ascorbic acid. Additionally, food processing techniques significantly affect nutrient bioavailability. Consequently, there is an urgent need for dietary interventions and processing strategies aimed at minimizing the inhibitory effects of anti-nutrients and enhancing micronutrient bioavailability to support better health outcomes.