Polylactide (PLA) and polycaprolactone (PCL) are biodegradable and bioabsorbable thermoplastic polymers considered as promising materials for oral applications. However, any abiotic surface used, especially in areas naturally colonized by microorganisms, provides a favorable interface for microbial growth and biofilm development. In this study, we investigated the biofilm formation of C. krusei and S. mutans on the surface of PLA and PCL immersed in the artificial saliva. Using microscopic (AFM, CLSM) observations and spectrometric measurements, we assessed the mass and topography of biofilm that developed on PLA and PCL surfaces. Incubated up to 56 days in specially prepared saliva and microorganisms medium, solid polymer samples were examined for surface properties (wettability, roughness, elastic modulus of the surface layer), structure (molecular weight, crystallinity), and mechanical properties (hardness, tensile strength). It has been shown that biofilm, especially S. mutans, promotes polymer degradation. Our findings indicate the need for additional antimicrobial strategies for the effective oral applications of PLA and PCL.