This study investigates the synergistic application of shear homogenization and pH-shifting to enhance the solubility and functional properties of insoluble co-products (CSIPA) derived from enzymatic hydrolysis of chia seed meal protein across varying durations. The modified CSIPA diverged markedly from its native counterpart in both physicochemical properties and architecture, correlating with the duration of enzymatic hydrolysis. The amino acid profiles changed, with all 17 hydrolyzed amino acids increasing and hydrophobic amino acids rising by 2.64 %–7.9 % compared to the untreated sample. Thermal stability improved, with increased enthalpy (5.33 %–15.98 %), denaturation (0.44–9.07 °C), and glass transition temperatures (7.96–27.45 °C). Particle size decreased (from 200 nm to 100 nm), and absolute ζ-potential rose from 10 mV to 30 mV with the extension of hydrolysis time. Multispectral analysis revealed blue or red-shifted peaks with altered intensities. CSIPA-12-7 derived from 100 min of enzymolysis had good functional properties, including foamability (222.67 ± 1.96 %), foaming stability (67.56 ± 0.77 %), emulsifying activity index (60.40 ± 0.82 m²/g), emulsion stability index (29.70 ± 0.31 %), and reduced interfacial tension (35.72 ± 0.70 %). Emulsions stabilized by the CSIPA-12-7 samples had the smallest particle size (18.26 ± 0.30 μm), the highest absolute ζ-potential (22.47 ± 0.72 mV), and uniform droplet microstructure. These results demonstrated that homogenization and pH-shifting enhanced the structure and functional characteristics of CSIPA, with a longer hydrolysis time expanding its application potential. This study supports the high-value utilization of chia seed meal protein byproducts and offers technical guides for sustainable development in the plant protein industry.