Photobioreactors for wastewater treatment coupled with nutrient recovery from the biomass is a promising biorefinery platform but requires working with microalgae-bacteria consortia. This work compares the effect that hydrolysis time and different enzymes have on the solubilization and recovery of components from microalgae-bacteria grown in piggery wastewater and microalgae grown in synthetic media by enzymatic hydrolysis. Higher carbohydrate solubilizations were obtained from microalgae-bacteria than from pure microalgae (38.5% vs. 27% Celluclast, 5 h), as expected from the SEM images. Proteases solubilized xylose remarkably well, but xylose recovery was negligible in all experiments. Alcalase hydrolysis (5 h) provided the highest peptide recovery from both biomasses (≈34%), but the peptide sizes were lower than 10 kDa. Low peptide recoveries (<20%) but larger peptide sizes (up to 135 kDa) were obtained with Protamex. Pure microalgae resulted in remarkably higher losses, but similar amino acid profiles and peptide sizes were obtained from both biomasses.