Spirulina biomass has great nutritional value, but its proteins are not as well adsorbed as animal ones are. New functional food ingredients and metabolites can be obtained from spirulina, using different selective biodegradations of its biomass. Four enzyme-assisted extraction methods were independently studied, and their best operation conditions were determined. Enzymes were employed to increase the yield of easily adsorbed proteic extracts. A biomass pre-treatment using Alcalase® (pH 6.5, 1% v/w, and 30 °C) is described, which increased the extraction yield of hydrophilic biocomponents by 90% w/w compared to the simple solvent extraction. Alcalase® gives rise to 2.5–6.1 times more amino acids than the others and eight differential short peptides (438–1493 Da). These processes were scaled up and the extracts were analyzed. Higher destruction of cell integrity in the case of Alcalase® was also visualized by transmission electron microscopy. The described extractive technology uses cheap, commercial, food grade enzymes and hexane, accepted for food and drug safety. It is a promising process for a competitive biofactory, thanks to an efficient production of extracts with high applied potential in the nutrition, cosmetic, and pharmaceutical industries.