Low-energy hydrogen-ions and tetrafluoromethane-ions produced from a gas discharge ion source were irradiated to poly(ethylene glycol-co-1,3/1,4 cyclohexanedimethanol terephthalate) (PETG) sheets for enhancing paint adhesion. The ion beams were characterized using a cast steel mass spectrometer, while the untreated and treated samples were characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, contact angle measurements, and profilometry. The paint adhesion was determined by using the standard method for evaluating adhesion by knife [ASTM D6677-07, Standard Test Method for Evaluating Adhesion by Knife (ASTM International, West Conshohocken, PA, 2012)] and was correlated with the calculation of the work of adhesion derived from the Young–Dupré equation. After plasma treatment, a significant decrease in the contact angle was observed in all samples, except for the CF4 ion-treated samples with the discharge current of 3 mA and an irradiation time of 30 min. At longer irradiation times, the treated samples showed lesser changes in the contact angle measurement. The increase in the average and root-mean-square surface roughness was observed on the samples after plasma treatment. The samples treated with either H2 or CF4 ions for 15 min showed a direct correlation between the discharge current and surface roughness. The samples treated for 30 min showed no significant correlation between the surface roughness and discharge current, which can be attributed to the possible melting of the samples since PETG has a low melting point. The observation made in this study on the relationship of wettability and surface roughness is consistent with the Wenzel wetting mode. Scanning electron micrographs showed surface etching on the hydrogen ion-treated samples while no significant surface changes were observed for the CF4 ion-treated samples. In general, paint adhesion was stronger for samples that exhibited enhanced wettability and high work of adhesion. The optimal work of adhesion to double the paint adhesion performance was at least 84.79 mN/m. The increase in the surface roughness after the treatment provided an increased friction between the paint and the PETG surface. The increase in the paint adhesion was also due to the covalent, hydrogen, and van der Waals bonding that are typically observed for highly wettable surfaces.