The objective of this study was to analyze millet protein hydrolyzates and peptide fractions with molecular mass under 3.0 kDa obtained from grains treated with different temperature values as inhibitors of angiotensin-converting enzyme (ACE), α-amylase, and α-glucosidase activity. The protein fractions were hydrolyzed in vitro in gastrointestinal conditions and the highest degree of hydrolysis was noted for globulin 7S obtained from control grains (98.33%). All samples were characterized by a high peptide bioaccessibility index, which was 23.89 for peptides obtained from globulin 11S after treatment with 100 °C. The highest peptide bioavailability index was noted for peptides obtained from globulin 11S after the treatment with 65 °C (2.12). The highest potential metabolic syndrome inhibitory effect was determined for peptide fractions obtained from the prolamin control (IC50 for ACE and α-amylase was 0.42 and 0.11 mg/mL, respectively) and after the 100 °C treatment (IC50 for ACE and α-glucosidase was 0.33 and 0.12 mg/mL, respectively) and from globulin 11S after the 65 °C treatment (IC50 0.38 and 0.05 for ACE and α-glucosidase, respectively). The effect of these samples on endothelial cell HECa10 was determined. The sequences of potential inhibitory peptides were identified as GEHGGAGMGGGQFQPV, EQGFLPGPEESGR, RLARAGLAQ, YGNPVGGVGH, and GNPVGGVGHGTTGT.