This paper demonstrates a sequential partitioning method for isolating bioactive compounds from Chrysochromulina rotalis using a polarity gradient, replacing classic and hazardous solvents with greener alternatives. Seventeen solvents were evaluated based on their Hansen solubility parameters and for having a similar polarity to the solvents they would replace, four of which were selected as substitutes in the classic fractionation process. Considering the fatty acid and carotenoid recovery yields obtained for each of the solvents, it has been proposed to replace hexane (HEX), toluene (TOL), dichloromethane (DCM) and n-butanol (BUT) with cyclohexane, chlorobenzene, isobutyl acetate and isoamyl alcohol, respectively. In addition, cytotoxic activity was observed when the TOL and DCM solvent extracts were tested against tumour cell lines, demonstrating the antiproliferative potential of compounds containing, for example, fucoxanthin, fatty acids, peptides, isoflavonoids or terpenes, among others.