A green and effective method of microwave-assisted three phase partitioning (MWTPP) was developed for the extraction and purification of proteins from Chlorella vulgaris microalgae species. Five types of salts were investigated and ammonium sulphate was selected as the best to form a three phase system with t-butanol as the solvent. The optimal conditions for maximum protein recovery are as follow: ammonium sulphate concentration 30%, ratio of slurry to t-butanol 1:1, microwave time 120 s, microwave duty cycle 80%, microwave power 100W and microalgae biomass concentration 0.5 % w/w. Under the optimized conditions, the protein recovery yield from microalgae was found to be 63.2% with a separation efficiency of 67.2%. Compared to the TPP process and initial MWTPP process, the recovery yield was enhanced by 2.54 and 1.49 times, respectively. The FESEM characterization of the microalgae after MWTPP process also showed the potential effect of microwaves to disrupt the cell wall and release the biomolecules for ease of recovery. MWTPP represents an efficient, economic and environmentally friendly technique for the extraction of bioactive compounds from microalgae.