The purpose of this study was to evaluate the use of supercritical fluid extraction with cosolvent (SFE-co) as an alternative process in the extraction of lupin alkaloids. A sample of crushed Lupinus mutabilis Sweet seeds, with a high content of alkaloids, was treated using aqueous extraction (AQE) and SFE-co, where the effect of the operating conditions and the solvent in the SFE-co were evaluated applying a factorial design. Results showed that both methods reduced the content of total alkaloids in the lupin seed, ensuring its safe consumption. SFE-co got an extraction yield (39.19 ± 0.14 mg/g) comparable with AQE (39.22 ± 0.16 mg/g) at a temperature of 323 K, a pressure of 27 MPa, using as a solvent supercritical carbon dioxide (scCO2) and dilute ethanol solution, but limited to a fraction of the treated sample. SFE-co, unlike AQE, was able to keep the nutritional value of the lupin seeds, reducing the time process from 235 hr (AQE) to 2.5 hr, assuring the non-use of an excessive amount of water and hazardous solvents. Moreover, the fractions formed in the extraction vessel by SFE-co allowed the understanding of the extraction mechanism of different components from a complex matrix related to their chemical polarity. Practical Applications: This study shows that it is possible to remove lupin alkaloids with green technology as supercritical fluid extraction with cosolvents, reaching extraction yields comparable with the conventional method (aqueous extraction), keeping the nutritional value of the sample, saving time and resources. However, working with a larger quantity of material than the usual used in a laboratory showed an inhomogeneous extraction of alkaloids from the sample, limiting the optimal extraction yield to one of the fractions formed. This reveals a future problem in the use of this technology at an industrial level, where the characteristics of the extracts are not only important but also the material treated since, in the lupin industry, the debittered seed and the released alkaloids are useful in the food and pharmaceutical industries, respectively.