In this study, phase separation of aqueous solutions of tetrabutylphosphonium trimethylbenzensulfonate ([P₄₄₄₄][TMBS]) under microflow is utilized for simultaneous target-selective extraction and separation. A microchannel with well structures at the bottom is fabricated in a poly(dimethysiloxane) (PDMS) device. A mixture of protein samples containing [P₄₄₄₄][TMBS] is flowed through the device while it is heated. A protein favorable to be distributed to [P₄₄₄₄][TMBS]-rich phase is selectively extracted and trapped in the well structure. As the separated [P₄₄₄₄][TMBS]-rich phase has a smaller volume, the target analyte is thus enriched. Herein, the selective extraction and concentration of cytochrome c from an aqueous mixture of bovine serum albumin, horseradish peroxidase, and azurin is examined. Quantitative concentrations are confirmed based on the volume ratio of each phase determined by color-information-based colorimetry. Precise selection and control of phase-separable materials enhance the versatility of liquid–liquid phase separation for the highly-sensitive detection of biomaterials and metal ions in small amounts of samples.