The present study explored the bioactive properties (antioxidant, antihaemolytic and antibacterial properties) of hydrolysates produced from quinoa and amaranth protein isolates. Various hydrolysates were produced using different enzymes (Bromelain, Chymotrypsin and Protease) at various time of hydrolysis (2, 4, 6 h). The results revealed that highest ABTS and DPPH radical scavenging activities were demonstrated by 2 h and 4 h chymotrypsin generated quinoa and amaranth protein hydrolysates (QC-2 and AC-4), respectively. For antibacterial activity, the zone of inhibition increased with increase in time of hydrolysis when tested against Staphylococcus aureus and the highest inhibition was shown by 6 h bromelain generated amaranth protein hydrolysate (AB-6). Highest Salmonella typhimurium, Escherichia. coil and Enterobacter aerogenes inhibition was revealed by 4 h bromelain (QB-4), 4 h protease (QP-4) and 2 h protease (QP-2) generated quinoa protein hydrolysates, respectively, compared to other hydrolysates. Moreover, 6 h bromelain and protease generated amaranth and quinoa protein hydrolysates displayed highest antihaemolytic activity. The outcomes of this study suggested that antioxidant, antimicrobial and antihaemolytic properties were significantly improved upon hydrolysis of quinoa and amaranth proteins. Therefore, quinoa and amaranth protein hydrolysates could be considered as a promising source of bioactive peptides with potential health promoting benefits.