Physical features, bioactive compounds and total antioxidant capacity (TAC) of coloured quinoa varieties (Chenopodium quinoa Willd.) from Peruvian Altiplano were studied. Quinoa seeds did not show a pure red colour, but a mixture which corresponded to different fractal colour values (51.0-71.8), and they varied from small to large size. Regarding bioactive compounds, total phenolic (1.23-3.24 mg gallic acid equivalents/g) and flavonol contents (0.47-2.55 mg quercetin equivalents/g) were highly correlated (r = 0.910). Betalains content (0.15-6.10 mg/100 g) was correlated with L colour parameter (r = -0.569), total phenolics (r = 0.703) and flavonols content (r = 0.718). Ratio of betaxanthins to betacyanins (0.0-1.41) was negatively correlated with L value (r = -0.744). Whereas, high TAC values (119.8-335.9 mmol Trolox equivalents/kg) were negatively correlated with L value (r = -0.779), but positively with betalains (r = 0.730), as well as with free (r = 0.639), bound (r = 0.558) and total phenolic compounds (r = 0.676). Unexploited coloured quinoa seeds are proposed as a valuable natural source of phenolics and betalains with high antioxidant capacity.