Andean lupin (L. mutabilis) seeds, appreciated for their high protein and unsaturated lipid content, must undergo water debittering to eliminate alkaloids. The aim of this research was to investigate the effects of debittering and further technological treatments such as extrusion and spray-drying (with two different coating agents, gum Arabic and maltodextrin, at 6% w/w) on the antioxidants of three Andean lupin ecotypes. Tocopherols (mainly γ-tocopherol) and free phenolics (flavonoids, phenylethanoids, phenolic acids) were abundant in bitter seeds, while carotenoids were scarce. After debittering, the content of tocopherols and bound flavonoids slightly increased, carotenoids were unchanged but free phenolics and bound phenolic acids decreased by 76.2% and 50.1%. Compared to debittered samples, the extrusion did not modify tocopherols, slightly increased phenolics and marginally reduced (14.5%) carotenoids. Spray-drying diminished tocopherols, carotenoids and phenolics (30.0%, 35.4% and 48.4%), mainly because of processing conditions; the coating agent dilution effect was minimal. No differences between coating agents were observed. Nevertheless, in debittered, extruded and spray-dried flours the total tocopherol (319, 318, 211 mg/kg DM) and phenolic (1033, 1179, 531 mg/kg DM) contents were still high. In all flours, free phenolics represented the majority of total phenolics (79.8%–95.6%). Processed flours of L. mutabilis present valuable levels of antioxidant compounds.