Chlorella sorokiniana protein isolates were enzymatically hydrolyzed using pepsin, bromelain, and thermolysin, with their molecular characteristics and bioactivities determined. Thermolysin hydrolysates exhibited the highest degree of hydrolysis (18.08% ± 1.13%). The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) results showed that peptides with molecular weights <10 kDa were found in the hydrolysates compared to the protein isolates. Bioactivity assays revealed that pepsin peptide fraction <5 kDa showed the highest angiotensin-converting enzyme (ACE)-inhibitory (34.29% ± 3.45%) and DPPH radical scavenging activities (48.86% ± 1.95%), while pepsin peptide fraction <10 kDa demonstrated the highest reducing power with 0.2101% ± 0.02% absorbance. Moreover, antibacterial assessment revealed that pepsin hydrolysate and peptide fractions displayed inhibition to the test microorganisms. Overall, the present findings suggest that C. sorokiniana protein hydrolysates can be valuable bio-ingredients with pharmaceutical and nutraceutical application potentials.