Fluoropolymers are widely used as coatings for their robustness, water-repellence, and chemical inertness. In contact with water, they are known to assume a negative surface charge, which is commonly attributed to adsorbed hydroxyl ions. Here, we demonstrate that a small fraction of these ions permanently sticks to surfaces of Teflon AF and Cytop, two of the most common fluoropolymer materials, upon prolonged exposure to water. Electrowetting measurements carried out after aging in water are used to quantify the density of ‘trapped’ charge. Values up to −0.07 and −0.2 mC m−2are found for Teflon AF and for Cytop, respectively, at elevated pH. A similar charge trapping process is also observed upon aging in various non-aqueous polar liquids and in humid air. A careful analysis highlights the complementary nature of electrowetting and streaming potential measurements in quantifying interfacial energy and charge density. We discuss the possible mechanism of charge trapping and highlight the relevance of molecular scale processes for the long term stability and performance of fluoropolymer materials for applications in electrowetting and elsewhere.