Alcohol–salt aqueous two-phase systems (ATPS) have shown promising results in the primary recovery of fucoxanthin from microalgae. However, the need of further operations to continue with the purification of the compound is required. In this sense, the use of ultrafiltration to process an ethanolic ATPS stream where fucoxanthin is recovered is explored in this work. Addition of ethanol to the original recovered ATPS ethanolic stream to a final relation of 74.15 % (w/w) resulted in the reduction of fucoxanthin unspecific losses in the membrane while incrementing its recovery. In fact, the ultrafiltration processing of the diluted ATPS sample presented a reduction of approximately 16 % of the proteic impurities, increasing product purity with a recovery of about 63 % of the compound in the permeate. These results show the potential of ultrafiltration in recovering molecules from ATPS streams in an easy-to-implement and economical manner avoiding a major setback in the industrial implementation of this unitary operation.