The partition behavior of small compounds in aqueous two-phase systems (ATPS) is less characterized (compared to biomacromolecules), since the liquid-liquid fractionation of such compounds is commonly done on organic-aqueous biphasic systems. In this study, five standard compounds (iohexol, salicin, chlorogenic acid, epicatechin, and gallic acid) were selected to evaluate the application of four types of ATPS for the fractionation of low-molecular weight compounds. Polyethylene glycol-salt, 1-ethyl-3-methylimidazolium acetate-salt, and ethanol-potassium phosphate ATPS achieved recovery yields higher than 75% in most cases. This study proves that ATPS can be applied efficiently for the recovery of small bioactive molecules of commercial interest.