This work aims at exploring new sustainable separation processes based on ionic liquids. Aqueous biphasic systems (ABS) based on poly(ethylene glycol) (PEG) with low molecular weight (600 and 4000 g mol–1) and cholinium-based ionic liquids and salts containing anions derived from carboxylic acids (oxalate, malonate, succinate, l-malate, fumarate, glutarate and citrate), available in natural compounds, are here presented. Contrary to common ionic liquids, the cholinium-based ionic liquids used in this work are biodegradable, nontoxic, cheap, and simple to prepare, and PEG is also a cheap and nontoxic phase promoter agent. The data reported in this work allows novel insights into the phase splitting mechanism of these ABSs regarding the influence of alkyl chain length of the anion and the presence of substituent groups in the anion. The effect of PEG molecular weight in the ABS was also addressed. Furthermore, the possible application of these systems for the extraction/separation of antioxidants, namely, tert-butylhydroquinone (TBHQ), was evaluated.