Multistage counter-current liquid–liquid extraction (MCCE) is a common unit operation in the chemical industry, but the technique is often difficult to use at laboratory and small production scales, because most MCCE systems are gravity-driven and require a large volume (∼100 mL). We present a new MCCE design that integrates segmented flow mixing and membrane-based phase separators to achieve equilibrium extraction at each stage. Multichannel peristaltic pumps transfer fluids from stage to stage in a counter-current manner, rather than dedicated pumps at each stage. A self-tuning pressure control element incorporated into each separator allows robust operation, even in the presence of variation between stages and imprecise pumping. Experimental data from two classical ternary case studies (toluene–acetone–water and ethyl acetate–acetic acid–water) compare well to ASPEN Plus simulations, showing that the extraction efficiency is ∼100%, regardless of the number of stages. Finally, we demonstrate the efficiency of the small-scale MCCE system (∼2 mL/stage) with an industrial example of recovery of THF and ethyl acetate from methanol, ethanol, iso-butanol, and tert-butanol mixtures.