Polyphenols are natural compounds with enhanced antioxidant properties. They are present in relatively high concentrations in fruit/vegetable by-products. Therefore, there is a need for the development of efficient and cost-effective methods for the separation and purification of these valuable compounds. Traditional extraction with organic solvents needs to be switched to novel methods that are more efficient, with reduced extraction times and low consumption of organic solvents. Aiming at developing sustainable processes for the separation and purification of phenolic compounds, we used three model compounds, namely resveratrol, quercetin, and gallic acid, to investigate ionic liquid-based aqueous biphasic systems (IL-ABSs) formed by cholinium-based IL in combination with polypropylene glycol with a molecular mass of 400 g/mol (PPG400). The ABS composition in the two-phase region was selected according to a previously determined phase diagram. Extraction studies indicated the preferential partition of resveratrol and quercetin toward the hydrophobic PPG-rich phase that is mainly dominated by its hydrophobic nature and the strong salting-out effect of ILs. On the other hand, due to its considerably hydrophilic nature, gallic acid preferentially migrates toward the IL phase. The achieved results from grape stem extract demonstrated high extraction efficiencies of cholinium dihydrogen phosphate (~99% for resveratrol for the PPG phase and 78% for gallic acid for the IL phase), with considerable selectivity, demonstrating promising outcomes for potential applications.