Microalgae is one of the most promising bio-based sources. It does not compete for arable land; can be cultivated in marine and fresh water and contains high amount of valuable biomolecules. However, microalgae production at a commercial scale is hindered by the high costs of cultivation and biorefinery. Currently, microalgae biorefineries focus on one-single product and specific markets (e.g. high value pigments and specialty chemicals), wasting and devaluating the remaining of the biomass. Therefore, novel technologies able to simplify the extraction process of multiple products and integrate different unit operations in an efficient and clean manner are needed. In this PhD thesis a liquid-liquid extraction technology named aqueous two phase systems (using ionic liquids as green solvents) was studied in its ability to extract and fractionate proteins, carbohydrates, pigments and lipids. The potential of this technology was demonstrated by its application in multiproduct and integrated biorefineries