Microalgae biorefinery has become an attracting topic to fully exploit the intracellular compounds such as lipids, proteins, polysaccharides or pigments, etc. Conventionally, microalgae biorefinery involves four major operations; harvesting, cell disruption, fractionation and purification, and final product formulation. This study evaluates the possibility to recover lipids and hydrosoluble compounds from Parachlorella kessleri cultivated in starving conditions. The cell disruption by bead-milling was coupled with centrifugation and membrane filtration for the fractionation. The impact of the biomass variation and the bead-milling, centrifugation and physico-chemical conditions on the compounds’ recovery into the supernatant and on the filtration performances was investigated. Three different filtration conditions were also compared: dead end, cross-flow and dynamic filtration. Finally, the best scenario allowed to recover 23% of the total lipids from initial biomass in the retentate and 9% of the sugars and 8% of the proteins from the biomass, totally soluble in the permeate.