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Titanium(IV) oxide (TiO2) and zirconium(IV) oxide (ZrO2) are well-known materials for their biocompatibility, hydrophilicity, antimicrobial activity, and excellent mechanical properties. Polymethyl methacrylate (PMMA), on the other hand, has many applications in medicine, biomedical systems, and engineering. However, its poor surface and mechanical properties limit its applications. The purpose of this study is how functionalization of PMMA would provide surface protection and reduce microbial adherence and biofilm formation. Hence, low-temperature Atomic Layer Deposition (ALD) was used to deposit TiO2, ZrO2, and TiO2/ZrO2 mixed oxides nanofilms on PMMA substrates. Surface composition was examined and Ti:Zr ratios were calculated through x-ray photoelectron spectroscopy. The coatings increased wettability and slightly enhanced nanohardness of PMMA. No significant change was observed in the surface roughness of PMMA after ALD. The nanocoatings protected the PMMA surface from thermal and brushing challenges by maintaining wettability, surface roughness, and film integrity. Additionally, compared to control, the mixed oxides with 1:2 cycle ratio of TiO2:ZrO2 showed a significant reduction on all bacterial and fungal initial adhesion and biofilm formation, while the TiO2 film provided reduction at initial fungal adhesion. Thus, TiO2/ZrO2 ALD on PMMA could enhance its surface, mechanical, and biological properties, preparing it for biomedical and engineering applications.