This study determined the physicochemical properties (apparent viscosity (ηapp), turbidity (A550nm), particle size and molecular mass distribution) of hydrolysates generated from whey protein concentrate (WPC), milk protein concentrate (MPC) and sodium caseinate (NaCN), following incubation with Debitrase HYW20™ and Prolyve™ at 50 °C, pH 7.0 for 1 and 4 h, before and after heat inactivation (80 °C for 10 min). The degree of hydrolysis (DH) increased with incubation time, giving values of 6.56%, 8.17% and 9.48%, following 1 h hydrolysis of WPC, MPC and NaCN with Debitrase HYW20™, and 12.04%, 15.74% and 17.78%, respectively, following 4 h incubation. These DHs were significantly higher compared to those obtained following 4 h incubation with Prolyve™. Hydrolysis with Debitrase HYW20™ gave >40% of peptides with molecular masses < 1 kDa for all substrates, which was higher than the value obtained following hydrolysis with Prolyve™. The effect of hydrolysis on the physicochemical properties was substrate dependent, since ηapp decreased in WPC and NaCN hydrolysates, particle size decreased for all the substrates, with aggregate formation for MPC, and turbidity decreased in WPC and MPC hydrolysates, while it increased in NaCN hydrolysates. The physical properties of the hydrolysates were influenced by the enzyme thermal inactivation step in a DH-dependent manner, with no significant effect on turbidity and viscosity for hydrolysates at higher DHs.