Developing mixed systems with both plant‐ and animal‐based proteins is crucial to address the limitations in the techno‐functional properties of plant‐based proteins. While the impact of thermal co‐aggregation on mixed systems has been extensively studied, there is limited information on the effects of non‐thermal processes. Therefore, this study aimed to compare the effects of high hydrostatic pressure (HHP, 600 MPa–5 min) and heat (90°C for 60 min) treatments on the protein profiles in a mixed micellar casein (CN):pea protein (PPI) system, while also elucidating the interactions involved in the formation of protein aggregates. Our results showed that both HHP and heat treatments induced the formation of soluble protein aggregates through disulfide bonds. However, protein aggregation was less prominent after application of HHP. In both treatments, the aggregates primarily consisted of convicilin, vicilin, legumin and lipoxygenase. However, albumin PA2 did not contribute to HHP‐induced aggregates, and vicilin played a lesser role in their formation compared to heat‐induced aggregates. CN from the HHP‐treated CN:PPI sample did not participate in aggregate formation, as previously demonstrated after heat treatment. The presence of residual whey proteins in the CN ingredients explained the formation of CN‐whey protein aggregates after heat treatment and, to a lesser extent, after HHP treatment.