The medical industry often uses ceramic and polymeric coatings to safeguard metal substrates. However, more investigation is required to explore the implementation of ceramic coatings on polymer substrates and to determine their degradation and in vitro characteristics. This work involves applying zirconia coating onto the 3D-printed PEEK polymer substrate using the RF magnetron sputtering technique. With varying layer thickness and printing speed parameters, PEEK samples (S1, S2, S3, and S4) were 3D printed and coated with zirconia. The coated and uncoated samples were immersed in Fusayama artificial saliva solution for 30 days. Following immersion in artificial saliva, this study examined the corrosion of 3D-printed PEEK samples with and without coatings. Elemental mapping, field emission scanning electron microscopy, and X-ray photoelectron spectroscopy were employed to evaluate sample morphology and estimate the binding energy of possible compounds generated in the artificial saliva solution. In vitro assessments such as antibacterial studies were performed against E. coli and S. aureus, and cytotoxic analysis was performed using Human Wharton’s jelly-derived mesenchymal stem cells (WJ-MSCs) to determine cell proliferation. The results indicated that sample S3, printed with 0.15 mm layer thickness and 20 mm/s print speed coated with zirconia showed a better degradation rate of 9.01% whereas the other three samples S1, S2, and S4 coated with zirconia showed deterioration rates of 36.4%, 33% and 16% respectively. Sample S3 showed a better antibacterial activity as biofilm formation was absent and also showed cell viability of about 79% and hence can be considered as a viable option for dental applications.