Hydrolysis of protein by proteases produces small molecular weights (MWs) peptides as nanomaterials that are easily absorbed. This study investigated the physicochemical properties and antioxidant activity of three plant protein isolates (PIs) including soy, wheat and pea after multi-enzyme hydrolysis. The MWs, particle size and microstructure of PI hydrolysate (PIH) were determined by SDS-PAGE and MALDI-TOF-MS mass spectrometry, dynamic light scattering and transmission electron microscopy, respectively. Cell viability was determined in vitro using a mouse skeletal muscle cell line (C2C12) and crystal violet staining. The MWs and particle sizes of the three plant PIs were reduced after hydrolysis by three proteases (bromelain, Neutrase and Flavourzyme). The MWs of soy, wheat and pea PIH were 103.5–383.0 Da, 103.5–1146.5 Da and 103.1–1937.7 Da, respectively, and particle size distributions of 1.9–2.0 nm, 3.2–5.6 nm and 1.3–3.2 nm, respectively. All three plant PIHs appeared as aggregated nanoparticles. Soy PIH (100 μg/mL) provided better protection against H2O2-induced oxidative damage to C2C12 than wheat or pea PIH. In summary, soy PIH had the best antioxidant activity, and particle size than wheat PIH and pea PIH. Therefore, soy PIH might be a dietary supplement for healthy diet and medical applications.