Ionic-liquid-based aqueous biphasic systems (ABS) have been the focus of a significant amount of research in the last decade. However, only (moderately) toxic and poorly biodegradable ionic liquids have been explored hitherto. Focusing on the development of more benign and sustainable approaches, a novel class of ABS using cholinium-based ionic liquids is proposed. For the first time, it is shown that a large assortment of cholinium-based ionic liquids is capable of undergoing liquid–liquid demixing in the presence of aqueous solutions with strong salting-out species. In order to assess the applicability of these systems for separation purposes, the partitioning of two antibiotics and/or their hydrochloride forms was also investigated. Cholinium-based ABS are shown to be improved routes for the extraction of pharmaceuticals, achieving complete extractions in a single-step by way of the proper tailoring of the phase forming components and their concentrations in the aqueous media.