Gentle extraction of ingredients from raw materials is essential for high-quality food ingredients and can lead to reducing the use of water, chemicals, and energy in the extraction. For example, a simple aqueous extraction can yield a mixture of oil, in the form of a natural oil-in-water oleosome emulsion, and proteins. The oleosomes and proteins can then be further separated in a next step. We explored a continuous counter-current electrophoretic process that separates oleosomes and proteins based on their electrophoretic mobility by balancing an electric field with an opposing solvent flow. The separation is accomplished through the retention of the component with the higher electrophoretic mobility, the oleosomes, and the passage of the proteins, having lower mobility. The fluxes of oleosomes and proteins from rapeseed, after aqueous extraction, were analyzed as a function of the electric field (0–75 Vcm−1) and 1.2 ± 0.1 mLmin-1 solvent flow rate. At 50 Vcm−1, the permeation flux of proteins was 10-fold higher than that of oleosomes, as shown by the selectivity increasing to 9.84 from 1.90 at 25 Vcm−1. The difference in their flux promises to become more pronounced under an increasing treatment duration, but two main technical limitations, electrolysis-based pH alteration and membrane fouling, restrict further separation. We expect the listed challenges can be mitigated with the addition of electrode rinse chambers and the use of larger pore size membranes.