Ibuprofen separation from water by adsorption and pertraction processes has been studied, comparing 16 different membranes. Tailor-made membranes based on Matrimid, Ultem, and diaminobenzene/diaminobenzoic acid with various contents of zeolite and graphene oxide, have been compared to the commercial polystyrene, polypropylene, and polydimethylsiloxane polymeric membranes. Experimental results revealed lower ibuprofen adsorption onto commercial membranes than onto tailor-made membranes (10–15% compared to 50–70%). However, the mechanical stability of commercial membranes allowed the pertraction process application, which displayed a superior quantity of ibuprofen eliminated. Additionally, the saturation of the best-performing commercial membrane, polydimethylsiloxane, was notably prevented by atomic layer deposition of (3-aminopropyl)triethoxysilane.