Fractionation of complex matrices such as biomass into diverse functional biomolecules without disrupting the biomolecule functionalities is a real challenge. Known separation processes are designed for the recovery of single products such as hydrophilic proteins or hydrophobic pigments, discarding the other products as waste. Here we present a concept for one-step biorefinery of hydrophobic and hydrophilic biomolecules from complex matrices using an ionic liquid-based surfactant free emulsion stabilised by microgel particles, while maintaining the product integrity. We demonstrate the process by simultaneous extraction of pigments and proteins from a microalgae extract; the hydrophobic pigments are transferred to the ionic liquid droplets and the proteins to the aqueous continuous phase. In contrast to most solvent extraction procedures, with this concept, the proteins retain their nativity, opening up an extraction pathway to fully functioning proteins while harvesting hydrophobes. A perspective towards continuous operation of this novel process is presented.