Deoiled chia flour is an important protein-rich by-product of the chia oil industry. This work used green process subcritical water hydrolysis to hydrolyse chia seed protein from deoiled chia flour and compared it with alkali hydrolysis. The yields of total protein, total amino acids, and reducing sugars in the soluble hydrolysate products were examined in relation to the effects of the extraction conditions (reaction time and temperature). Hydrolysates generated at 225 °C after 30 min of hydrolysis exhibited the highest protein content (213.76 ± 0.44 mg/g of chia protein concentrate) and total free amino acid content (44.26 ± 0.79 mg/g of chia protein concentrate), while the highest extent of extraction (62.72 ± 1%), and degree of hydrolysis (13.85 ± 0.50%) was observed at 200 °C after 30 min of hydrolysis. Alkali hydrolysis exhibited significantly (p < 0.05) lower protein hydrolysis (10.66 ± 0.51%) and total free amino acids (22.66 ± 0.53 mg/g of CPC) than subcritical water hydrolysis. SEM, elemental analysis and XRD conferred the degradation of CPC and provided strong evidence in supporting subcritical water hydrolysis for chia seeds. Subcritical water hydrolysates can be envisioned to develop functional foods from chia seeds.