The cyanobacterium Spirulina platensis was subjected to a fractionation process involving ultrasound-assisted extraction and membrane filtration to obtain a pure phycocyanin fraction and a clarified colorless protein fraction free of chlorophyll and carotenoids. The effects of pressure and power on total protein release were assessed. The retention of the extracted proteins was then assessed by ultrafiltration, with and without ammonium sulfate precipitation. Total protein recovery yields reached 97% in aqueous solution, at a low frequency (12 kHz), atmospheric pressure, and with an ultrasonic power of 200 Watts (W). Ammonium sulfate (25% w/v) precipitation was used to remove pigments and impurities from the crude protein extract. Finally, semifrontal ultrafiltration resulted in high levels of C-phycocyanin recovery in the retentate: 95% and 91% with 10 and 100 kDa-cutoff membranes, respectively. However, the levels of total non-pigmented proteins in the permeate compartment did not exceed 67% with a 100 kDa-cutoff membrane. A fractionation process is proposed here for the valorization of two different protein fractions from Spirulina platensis.