The semi-solid wastes (pomace or alperujo) produced in the two-phase olive oil extraction process contains extremely high organic load and phenolic substances. Efficient treatment of such kinds of wastes using membrane filtration, should be sought to reduce the hazardous effects to the environment. On the other hand, phenolic compounds can be isolated and purified up to a level of commercial exploitation using the membrane technology. Firstly, the extraction process with mixtures of water and ethanol was optimized by testing extraction parameters (e.g., solvent’s mixture, duration, and temperature) at laboratory scale. Next, extraction was conducted using larger volumes and the treatment was continued in a pilot membrane filtration system, consisted of ultrafiltration (UF), nanofiltration (NF) and reverse osmosis (RO) membranes. The extracted solution from the olive oil pomace was fed to the pilot membrane filtration system, where all fat, lipids, and solids were removed while the phenolic compounds were concentrated in the retentate streams of NF and/or RO. Total phenolic content (TPC) at the RO’s concentrate stream was 225 mg/L and at the final effluent was lower than 10 mg/lt. The chemical oxygen demand (COD) value at the final effluent was much lower (~280 mg/L) than in the feed stream (>32,000 mg/L).