Andean lupin (Lupinus mutabilis) seeds are appreciated for their high protein and lipid contents and have potential applications as ingredients in food, cosmetic, and pharmaceutical industries. Nevertheless, the information about the seed composition (especially in lipophilic antioxidants) of ecotypes from distinct cropping areas is currently limited. Thus, the aim of the present research was to assess the morphological characteristics, chemical composition, tocopherol and carotenoid contents of the seeds of 33 Andean lupin ecotypes from different Peruvian regions, along with three L. albus, one L. angustifolius and one L. luteus controls. Significant differences were noted among the Andean ecotypes for all analyzed features. The protein, lipid and ash contents were 32.0–46.9, 13.6–18.6 and 2.7–4.4 g/100 g dry matter (DM), respectively. The seeds were rich in tocopherols (172.1–249.8 mg/kg DM; γ-tocopherol was 98% of total tocols) and low in carotenoids (0.69–2.89 mg/kg DM). Debittering increased the tocopherol content (227.0–378.2 mg/kg DM), probably because of the soluble components loss, although the carotenoid concentration remained unchanged. The Andean lupins had higher protein, lipid and tocopherol contents than L. albus and L. angustifolius; the L. luteus values were within the L. mutabilis range. These results suggest that L. mutabilis harbors nutritional characteristics that are well suited to modern food trends.