Lupinus mutabilisSweet is a fabaceous plant native to the Andean highlands and produces seeds with valuable nutritional properties. Thus, as part of our research on native emerging food, the present study aimed at determining some nutritional and functional-related features of seeds from twoL. mutabilisecotypes after propagation in two different substrates commonly found in the Bogotá plateau. Propagated plants produced seeds that, after conventional debittering, exhibited attractive contents of soluble protein (24–39 g/100 g dry seed powder (dsp)), phenolic (787–1003 g/100 g dsp), isoflavone (1–104 g/100 g dsp), and iron (5.3–6.4 g/100 g dsp), as well as antioxidant capacity (39–78 µM/100 g dsp). Higher pH, humidity saturation, organic matter, and total nitrogen of silty loam soil promoted isoflavone accumulation and better antioxidant capacity at pH 4–7, and no soil effect was observed for total phenolic and iron contents. The profiles based on isoflavone aglycones were also recorded by liquid chromatography-mass spectrometry, detecting eleven main compounds with mutabilein as the most abundant isoflavone (38.3–104.3 g/100 g dsp). Finally, a formulation was developed to fabricate an emulsion-type drink based on the debittered, pulverizedL. mutabilisseeds, resulting in different emulsifying capacities (19–100%) depending on the biopolymer stabilizer, being xanthan gum the best additive. The findings revealed an attractive Andean lupin profile to be used as a raw food material.