Aqueous biphasic systems constituted by ionic liquids (IL-based ABSs) are a target of investigation in the separation of high-value biomolecules. However, identification of the molecular-level mechanisms ruling the two-phase formation and extraction performance of these systems is crucial to the successful design of effective separation processes. In this work, IL-based ABSs formed by K2HPO4 and cholinium carboxylate ILs ([Ch] [CnCO2] with n = 1-7, comprising anions with odd and even alkyl chain lengths) were investigated. The corresponding ternary phase diagrams, including binodal curves, tie-lines, tie-line lengths, and critical points, as well as the Setschenow salting-out coefficients (k(s)), which quantitatively describe the two-phase formation ability, were determined at 298 K. The extraction capability of these systems was then evaluated for four amino acids (L-tryptophan, L-phenylalanine, L-tyrosine, and L-3,4-dihydroxyphenylalanine/L-dopa). It was found that ILs composed of anions with even alkyl chains display slightly higher k(s) values, meaning that these ILs are more easily salted out or more easily phase-separated to form ABSs, whereas ABSs formed by ILs with anions comprising odd alkyl chains lead to slightly higher partition coefficients of amino acids. Beyond the neat IL odd-even effect resulting from their nanostructuration, being this a well-known phenomenon occurring in a series of their thermophysical properties, the existence of an odd-even effect displayed by the IL anion aliphatic moiety in aqueous solution is shown here, visible in both the two-phase formation ability and extraction performance of ABSs. These findings contribute to elucidate of the molecular-level mechanisms governing ABS formation and partitioning of biomolecules, ultimately contributing to the design of proficient separation platforms.