SCOPE:Research is limited on diet challenges to improve health. A short-term, vegan protein diet regimen nutritionally balanced in macronutrient composition compared to an omnivorous diet was hypothesized to improve metabolic measurements of blood sugar regulation, blood lipids, and amino acid metabolism. METHODS AND RESULTS: This randomized, cross-over, controlled vegan verses animal diet challenge was conducted on 21 (11 female,10 male) healthy participants. Fasting plasma was measured during a 3-day diet intervention for clinical biochemistry and metabonomics. Intervention diet plans met individual caloric needs. Meals were provided and supervised. Diet compliance was monitored. CONCLUSIONS:The vegan diet lowered triglycerides, insulin and homeostatic model assessment (HOMA-IR), bile acids, elevated magnesium levels, and changed branched-chain amino acids (BCAAs) metabolism (p<0.05), potentiating insulin and blood sugar control after 48 hours. Cholesterol control improved significantly in the vegan verses omnivorous diets. Plasma amino acid and magnesium concentrations positively correlated with dietary amino acids. Polyunsaturated fatty acids and dietary fiber inversely correlated with insulin, HOMA-IR and triglycerides. Nutritional biochemistries, BCAAs, insulin and HOMA-IR were impacted by sexual dimorphism. A health-promoting, BCAA-associated metabolic signature was produced from a short-term, healthy, controlled, vegan diet challenge when compared with a healthy, controlled, omnivorous diet.