This Special Issue editorial summarizes 10 original articles and 4 reviews on amino acid metabolism beyond protein synthesis, covering methionine toxicity, nitric oxide pathways, and branched-chain amino acids in metabolic disease. Key findings include that high methionine intake induces anxiety-like behavior in mice, nitrate supplementation alters amino acid homeostasis, and essential amino acids with exercise protect against dexamethasone-induced muscle loss. The collection underscores amino acids as fundamental signaling molecules with clinical relevance across cardiology, neurology, endocrinology, and gastroenterology.