To engineer polymer surfaces with long-lasting wettability properties and with high coating stability in aqueous media, we investigated the surface wettability of polyethylene terephthalate (PET) films treated by radio frequency (RF) atmospheric-pressure plasma. By combining plasma activation and hexamethyldisiloxane (HMDSO)-based plasma polymerization, stable PET surface properties from highly hydrophobic to superhydrophilic were achieved. The results clearly showed that the wettability of PET surfaces could be tuned from stable high hydrophobicity (>140°) to stable superhydrophilicity (<10°) with a minimized aging effect by using plasma activation of plasma deposited coatings. Surface roughness increase and CH3 groups introduction are primarily responsible for the coating hydrophobization, while the introduction of more oxygen-containing polar functional groups is the main factor leading to superhydrophilization. Importantly, the coatings engineered by this unique combination showed high stability in water over 14 days. Overall, this work contributes to the easy-to-overlook links between plasma activation and plasma polymerization, demonstrates that atmospheric-pressure RF plasma can be a versatile tool to control surface properties of polymers in a wide range from high hydrophobicity to superhydrophilicity with high coating stability in aqueous media and a negligible aging effect, which is promising for emerging biomedical applications.