Bioactive compounds and nutritional characterization in three genotypes of mashua tubers (Tropaeolum tuberosum Ruiz and Pavón) from different agroecological areas of the Peruvian highlands (3747 at 3888 meters above sea level) were studied. The studied genotypes from different agroecological areas significantly differed for vitamins, amino acids, and bioactive compounds. However, the nutritional characteristics of yellow, purple, and yellow-purple mashua remained unaffected. Its tubers were shown to be important sources of protein and fiber. The nutritional analysis revealed high phosphorus and potassium values, as well as considerable amounts of vitamin C. The amounts of total free amino acids in the genotypes ranged from 2.73 ± 0.450  mg/g dry matter (DM) to 6.825 ± 0.450  mg/g DM. Important total anthocyanins, total flavonoids, total phenolics, tannin content, and antioxidant activity values were obtained from purple genotype. Unexploited colored mashua tubers are proposed as a valuable natural source of phenolics and anthocyanins with high antioxidant activity.