Neurodegenerative diseases—including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis—pose a growing challenge to global health due to their progressive course and limited therapeutic options. Emerging evidence suggests that functional food factors, such as flavonoids and vitamins, contribute significantly to neuroprotection. These bioactive compounds exert antioxidant activity and modulate the gut–brain axis, which may help delay the onset and progression of disease. This chapter explores the molecular neuropathological mechanisms underlying the protective effects of these compounds, focusing on their impact on amyloid aggregation (e.g., amyloid-β, tau, superoxide dismutase 1), oxidative stress, and protein supersulfidation. We also discuss recent clinical studies supporting their use as dietary interventions in disease prevention. Understanding the connection between nutrition and brain health may provide novel, noninvasive strategies for managing and mitigating neurodegenerative disorders through functional foods.