Ionic-liquid-based aqueous biphasic systems (IL-based ABS) have been broadly investigated for the separation of high-value compounds. Nevertheless, the large-scale application of IL-based ABS is still hampered by the high cost and hazardous features of most ILs used. Aiming at characterizing novel ABS composed of ILs with a more acceptable environmental footprint and enhanced biocompatibility, in this work, ABS formed by water, cholinium carboxylate ILs ([Ch][CnCO2], with n = 2 to 6), and K2CO3 were investigated. The respective ternary phase diagrams, including binodal curves, tie-lines, and critical points, were determined at (298 +/- 1) K and atmospheric pressure. The capability to form ABS (or of the IL to be salted-out) increased with the increase of the alkyl chain length of the IL anion up to cholinium pentanoate; however, for longer anion alkyl chain lengths the ILs self-aggregation led to a decrease of the ILs ability to form ABS. Furthermore, the liquid-liquid equilibrium data experimentally determined were modeled using the local composition activity model NRTL (nonrandom two liquid). The extraction performance of these systems was finally evaluated with four nitrogenous bases (thymine, adenine, guanine, cytosine). In all studied systems nitrogenous bases preferentially migrated to the IL-rich phase, with extraction efficiencies ranging between 81% and 97% in a single-step. The determined novel phase diagrams indicate the composition of the mixtures required to use IL-based ABS as separation routes. The extraction performance evaluation of these systems with nitrogenous bases provides an indication of their possible application to isolate high-value compounds with biotechnological interest.