Advances in biochemical and molecular manipulation have led to increased biomass productivity and oil accumulation in the microalgae C. reinhardtii. However, scalable processes for the recovery of oil and other valuable biomolecules, such as protein, from C. reinhardtii are scarce. The use of aqueous enzymatic extraction, a non-solvent and environmentally friendly bioproduct recovery method, provides an opportunity to design an integrated process for oil and protein fractionation to reduce bioenergy and bioproducts costs. Based on the mechanistic understanding of biomolecule distribution and compartmentalization, an aqueous enzymatic treatment for the release of internally stored lipid bodies was designed. Application of a C. reinhardtii-produced protease, autolysin, for lysis of the microalgae cell wall was followed by a secondary treatment with trypsin for chloroplast disruption and lipid body release. Protein recovery after the primary treatment with autolysin indicated a 50.1 ± 4.2% release of total soluble protein and localization of lipid bodies still in the chloroplast. The development of a secondary enzyme treatment (trypsin) for chloroplast and lipid body lysis demonstrated a high percent of remaining lipids (73 ± 7%) released into the supernatant. The results indicate that the application of an enzymatic treatment scheme for protein and oil recovery is a promising alternative to traditional extraction processes.