In this work, the structural and functional properties of proteins from black and yellow quinoa were assessed as well as the in vitro digestibility. Black quinoa flours contained higher amounts of crude fiber and lower amounts of total starch compared to the yellow counterpart. Structurally, electrophoretic SDS-PAGE bands corresponding to 50 kDa 11S globulin, and 55 kDa protein (under non-reducing conditions), and 31–33 kDa (under reducing conditions) were observed in both isolates. Fat absorption and water solubility indexes were comparatively lower in the black quinoa protein isolate. Both isolates showed a good nitrogen solubility index and emulsifying activity. In vitro protein digestibility was similar for both varieties (>95%). The addition of the protein isolates obtained from quinoa flours could be considered as a good alternative to increase the protein content of different foods taking advantage of key functional properties such as nitrogen solubility index and emulsifying activity.