UV–digital printing belongs to the commonly used method for custom large-area substrate decoration. Despite low surface energy and adhesion, transparent polymer materials, such as polymethylmethacrylate (PMMA) and polycarbonate (PC), represent an ideal substrate for such purposes. The diffuse coplanar surface barrier discharge (DCSBD) in a novel compact configuration was used for substrate activation to improve ink adhesion to the polymer surface. This industrially applicable version of DCSBD was prepared, tested, and successfully implemented for the UV–digital printing process. Furthermore, wettability and surface free energy measurement, X-ray photoelectron spectroscopy, atomic force, and scanning electron microscopy evaluated the surface chemistry and morphology changes. The changes in the adhesion of the surface and of ink were analyzed by a peel-force and a crosscut test, respectively. A short plasma treatment (1–5 s) enhanced the substrate’s properties of PMMA and PC while providing the pre-treatment suitable for further in-line UV–digital printing. Furthermore, we did not observe damage of or significant change in roughness affecting the substrate’s initial transparency.