BACKGROUNDMicroalgal biomass is generally used to produce a single product instead of valorizing all of the cellular components. The biomass production and downstream processes are too expensive if only one product is valorized. A new approach was proposed for the simultaneous and selective partitioning of pigments and proteins from disrupted Neochloris oleoabundans cultivated under saline and freshwater conditions. RESULTSAn aqueous two-phase system composed of polyethylene glycol and cholinium dihydrogen phosphate selectively separated microalgal pigments from microalgal proteins. 97.31.0% of lutein and 51.6 +/- 2.3% of chlorophyll were recovered in the polymer-rich phase. Simultaneously, up to 92.2 +/- 2.0% of proteins were recovered in a third phase (interface) in between the aqueous phases (interface). The recovered proteins, including Rubisco with a molecular weight of approximate to 560kDa, seem to be intact and pigments did not suffer degradation, demonstrating the mildness of this system for fractionating microalgal biomolecules. CONCLUSIONThe ability of aqueous two-phase systems (ATPSs) to simultaneously and efficiently fractionate different biomolecules in a mild manner from disrupted microalgae is demonstrated. This is an important step towards the development of a multiproduct microalgae biorefinery. (c) 2018 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.