In the last decades, microalgal biomasses as a source of bioactive compounds represented an object of interest for researchers. To this end, studies were carried out on the extraction processes for the recovery of high value-added molecules. The excessive use of hazardous organic solvents and the growing environmental concern, led to the exploration of new extraction routes. Among these, innovative green solvents, such as natural deep eutectic solvents (NaDES) were studied. However, the difficulty of the fractionation NaDES microalgal extracts in separate streams rich in lipids, proteins, carbohydrates still represents a major drawback for a possible industrial application. In the present contribution, the feasibility to use aqueous two-phase systems (ATPS) for the fractionation of the main bioactive compounds (lipids, proteins, carbohydrates) contained in a NaDES extract from the green microalga Chlorella vulgaris was explored. Furthermore, a process flow diagram, containing a three-stage separation unit of ATPS, formulated with two aqueous solutions of polyethylene glycol 600 and choline chloride, was designed. Overall, the process designed, allowed obtaining separation yields higher than 70 %.