The surface of dental materials is exposed to various prophylaxis protocols during routine dental care. However, the impact of these protocols on the functional properties of the material’s surface remains unclear. This study investigates the influence of different dental prophylaxis protocols on the surface properties and their effect on the mechanical performance of CAD-CAM restorative materials. Discs (Ø = 15 mm, thickness = 1.2 mm) were fabricated from resin composite (RC, Tetric CAD), leucite-reinforced (LEU, IPS Empress CAD), lithium disilicate (LD, IPS e.max CAD), and zirconia ceramics (ZIR, IPS e.max ZirCAD MT). The materials were subjected to six prophylactic treatments: untreated (CTRL), prophylactic paste fine (PPF), prophylactic paste coarse (PPC), pumice stone (PS), air abrasion with sodium bicarbonate jet (BJ), and ultrasonic scaling (US). Biaxial flexural fatigue tests, along with fractographic, roughness, and topographic analyses, were conducted. No significant changes in fatigue strength were observed for RC, LD, and ZIR under any prophylaxis protocols. However, LEU subjected to BJ treatment exhibited significantly reduced fatigue strength (p = 0.004), with a 22% strength reduction compared to the monotonic test and substantial surface alterations. Surface roughness analyses revealed increased roughness for RC treated with PPF, PPC, and PS compared to CTRL (p < 0.05), while LD exhibited decreased roughness following PPF, PS, and US treatments (p < 0.05). In ZIR, only the BJ protocol increased roughness (p = 0.001). In conclusion, dental prophylaxis protocols do not significantly affect the mechanical strength of RC, LD, and ZIR materials, thus allowing any protocol to be used for these materials. However, for LEU ceramics, the BJ protocol should be avoided due to its effect of reducing fatigue strength and damaging the surface.
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