Tropaeolum tuberosum Ruíz and Pav. “Mashua” is a crop from the Andean region associated with preventing chronic degenerative diseases. This study evaluated the content of bioactive compounds (phenolics, glucosinolates, carotenoids, and ascorbic acid) in twenty-seven Peruvian mashua morphotypes. Furthermore, three morphotypes (MAC 067, MAC 092, and MAC 123) were selected to evaluate further the effect of methyl jasmonate (MeJA) on the accumulation of bioactive compounds. Phenolic content in the mashua morphotypes ranged from 2990.76 ± 273.5 mg/kg to 24,217.36 ± 1144 mg/kg; whereas carotenoids ranged from 12.8 ± 0.6 mg/kg to 85.8 ± 3.1 mg/kg. Moreover, total glucosinolate content ranged from 65 ± 11 mmol/kg to 1289 ± 65 mmol/kg. The different mashua morphotypes showed low levels of ascorbic acid (lower than 5 mg/kg) compared with other crops. Except for glucosinolates, MeJA application augmented the level of bioactive compounds, showing increases of up to 150.1%, 535.0%, and 542% for total phenolics, carotenoids, and ascorbic acid, respectively. Results indicated that mashua is an excellent source of phenolics and glucosinolates, whereas it contains adequate levels of carotenoids and low levels of vitamin C. MeJA application during postharvest represented a simple approach to increase the content of bioactive compounds in mashua.