Though widely used in the Andes in the ancient times, canihua has been considered a forgotten crop for a long time. Only lately, due to increasing demand in European countries, canihua reveals significantly growing market potential. With the current scarcity of research about the composition, nutritional and healthy profile, this study aimed to provide new information about the antioxidant capacity and the fatty acid profile of Bolivian canihua cultivars with different grain colour. Samples of 28 cultivars were used in the study, divided into three groups according to the grain colour– light brown, pink and dark brown. Total antioxidant capacity, content of the total phenols and flavonoids, as well as fatty acid composition were quantified for the groups. The cultivars with light brown grains displayed the strongest antioxidant potential and the highest content of phenols and flavonoids. Regardless of the colour, canihua cultivars were rich in saturated fatty acids, linoleic and oleic acid. The pink grained cultivars displayed the most favourable fatty acid profile, with lowest amount of C16:0. Correlation analysis showed that total phenols and flavonoids, as well as saturated and monounsaturated fatty acids had strong and positive contribution for the antioxidant potential of the canihua grains.