BackgroundNatural polymers are macromolecules produced by living organisms, with a wide range of applications and relevance for the development of a circular economy. However, large‐scale production is still hindered by several factors, such as downstream processing. In this work, three‐phase partitioning (TPP) systems were investigated for separation of model polysaccharide (dextran, alginate and gum arabic) from protein (Bovine serum albumin (BSA) and lysozyme). The recyclability of phase‐forming compounds used to form the extractive platform was assessed by ultrafiltration (UF). This study contributes to development of production processes for biopolymers from fermented waste by proposing an effective separation technique for fractionation of biopolymers. Previously such biopolymers were only collected as mixtures, and with the studied approaches, also fractionation may be applied of polysaccharides from proteins. With the chosen systems, the scope of TPP systems is expanded by using another class of phase‐forming compound (polymers), and in addition, UF was studied as a versatile regeneration approach.ResultsWithin the TPP approach, the best separation of dextran from BSA was achieved using TPP systems composed of 25 wt% PEG + 25 wt% K3C6H5O7 and 36 wt% EtOH + 10 wt% K3PO4, in which more than 95% of dextran and BSA were found as precipitate and partitioned to top phase (PEG or EtOH‐rich), respectively. By using other model compounds, it was found that the molecular weight and charge of biopolymer play a key role in the yield and selectivity of TPP systems. Finally, by using ultrafiltration/diafiltration, about 99% of ethanol and phosphate salt used to form the extractive platform could be retrieved in the permeate stream.ConclusionThe high extraction yields, selectivity and recyclability of phase‐forming compounds confirm the potential of polymer‐based and alcohol‐based TPP systems to fractionate biopolymer mixtures.This article is protected by copyright. All rights reserved.