Background <p>Nutrition has a profound impact on male reproductive well-being through its influence on molecular mechanisms involved in spermatogenesis, sperm function, and endocrine regulation. Elucidation of these nutrition–fertility relationships at the molecular level may inform future research directions, although clinical application remains uncertain. The review critically assesses how nutritional interventions regulate gene expression, protein synthesis, and cellular signaling pathways controlling sperm concentration, motility, morphology, and DNA integrity.</p> Main body <p>This review discusses molecular mechanisms connecting nutritional components to male fertility results. Micronutrients such as vitamins C, D, E, zinc, selenium, and folate have been implicated in oxidative stress regulation through molecular processes, primarily based on preclinical and observational evidence. Zinc has been primarily shown in experimental and observational studies to act as a cofactor in enzymes of testosterone biosynthesis, preserve sperm membrane phospholipid integrity through metallothionein binding, and modulate flagellar dynein ATPase activity; however, randomized controlled evidence remains limited. In mechanistic and animal studies, Omega-3 fatty acids, particularly DHA, are incorporated into sperm membrane phospholipids in mechanistic and animal models, increasing membrane fluidity and influencing mitochondrial respiratory chain efficiency through cardiolipin modification; while human interventional findings remain heterogeneous. Mechanistic data indicate that Vitamin C quenches hydroxyl radicals as an electron donor, whereas coenzyme Q10 facilitates efficient mitochondrial electron transport, together inhibiting oxidative damage to sperm DNA; although clinical benefits are not consistently demonstrated. However, diets high in processed foods and saturated fats have been associated with increased lipid peroxidation and inflammatory signalling, which may adversely influence spermatogenesis, potentially involving epigenetic regulation.</p> Methods <p>A scoping narrative literature review was conducted using PubMed, Scopus, and Web of Science (January 2000–March 2025). Human, animal, and in vitro studies examining nutritional exposures, molecular mechanisms, and semen parameters were included.</p> Conclusion <p>This review synthesizes molecular evidence linking nutrition to male fertility through defined biochemical and cellular pathways. By critically evaluating supportive, null, and context-dependent findings, it highlights where mechanistic data align with clinical observations and where translation remains limited. This study identifies key gaps in long-term adaptation, nutrient–gene interactions, and dose–response relationships, underscoring the need for well-designed clinical trials incorporating validated molecular biomarkers. The existing literature is predominantly derived from preclinical and observational studies, with limited high-quality randomized controlled trials. Future research integrating nutrigenomics and epigenetic mechanisms will be essential to determine whether targeted nutritional strategies can be reliably applied in male reproductive health before routine clinical implementation can be recommended.</p>