Metabolic problems, aging, and age-related illnesses like insulin resistance, obesity, sarcopenia, and neurodegeneration are all significantly influenced by mitochondrial dysfunction. Foods that have been shown to have physiological or therapeutic benefits are known as clinical foods, and they have gained attention as possible modulators of mitochondrial function. To improve cellular energy homeostasis and lower oxidative stress, bioactive substances as polyphenols, omega-3 fatty acids, sulforaphane, curcumin, and epigallocatechin gallate can affect mitochondrial biogenesis, mitophagy, oxidative phosphorylation, and NAD⁺ metabolism. The gut-mitochondria axis, where metabolites originating from the microbiota influence mitochondrial pathways that connect metabolism, immunity, and nutrition, was highlighted by recent research. In addition to discussing molecular mechanisms and signaling pathways, this article highlights the most recent research on clinical diets that target mitochondrial function and briefly describes their potential therapeutic uses.