Soy protein concentrate (SPC) was hydrolyzed using several commercial food-grade proteases (Alcalase, Neutrase, papain, Everlase, Umamizyme, Flavourzyme) and their combination to obtain promising ingredients in the manufacture of functional bakery products. In all cases, the hydrolysis caused nutritional, sensory, and rheological changes in SPC, as well as protein structural changes like increased surface hydrophobicity and content of exposed SH groups with the magnitude of these changes depending on enzyme specificity. The hydrolysis with the combination of Neutrase and Flavourzyme (NeuFlav) increased essential amino acid content by 9.8% and that of Lys by 32.6% compared to SPC. This hydrolysate showed also significant antioxidant activities including ABTS and superoxide anion scavenging activity and metal-chelating ability. The addition of all hydrolysates in wheat flour decreased water adsorption and increased development time to some extent due to gluten network weakening, but also decreased the rate of starch retrogradation, contributing to the increase of the shelf-life of bakery products. The NeuFlav tasted less bitter than other hydrolysates, while E-nose provided a discrimination index of 93 between control and hydrolysates. It appeared that the addition of the NeuFlav hydrolysate in a cookie formulation improved protein content and nutritional quality and directed to its higher general consumer acceptability than cookies formulated with only wheat flour.