Aqueous biphasic systems (ABS) based on Pluronic L-35, a (EO) x -(PO) y -(EO) x triblock copolymer, were determined and applied in the separation of two structurally similar flavonoids (naringin and rutin). Two sets of phase formers were paired with Pluronic L-35, one comprising conventional salts/buffer and other including cholinium-based ionic liquids (ILs). It is shown that while the conventional salts induce an unbalanced and strong salting out leading to complete extraction of flavonoids to the same phase in most of the cases (84.7 ± 0.6% ≤ R NAR ≤ 100% and 53.2 ± 0.5% ≤ R RUT ≤ 99.7 ± 0.1% with selectivities ranging from 1 to 11.8), the cholinium-based ILs provide an enhanced extractive performance. Indeed, these novel cholinium ILs/ Pluronic L-35-based ABS allowed the manipulation of the affinity of both naringin and rutin to opposite phases, thus yielding a selective separation. The best results were achieved for the system using [Ch][Bic] as phase former (R NAR = 89.6 ± 0.3 and R RUT = 32 ± 2 with a selectivity of 18.9). An integrated approach based on the sequential implementation of Na 2 SO 4 /Pluronic L-35-(step 1) and [Ch][Bic]/Pluronic L-35-based (step 2) ABS was designed to purify the flavonoids from a complex synthetic mixture simulating natural extracts. Remarkably, glucose (the main contaminant) was removed during step 1 with an extraction efficiency of 60 ± 4% to the Na 2 SO 4 -rich phase, while step 2 has enabled the efficient separation of naringin from rutin.