This study aimed to investigate the effect of various periodontal hygiene procedures on the surface properties of direct and indirect restorative materials. Disc-shaped specimens (10 × 2 mm) of FC: Flowable Composite, UC: Universal Composite, IC: Indirect Composite, CC: CAD/CAM Composite were fabricated (n = 70) and divided randomly into subgroups: 1-Control, 2-US: Ultrasonic scaling, 3-RP: Rubber-cup polishing, 4-AP: Air-polishing, 5-US+RP, 6-US+AP, 7-US+AP+RP. The color, surface roughness, and gloss measurements were performed. Data were analyzed with variance analysis and the correlation coefficient was used to evaluate the relationship between surface properties (p < 0.05). The highest and lowest roughness values were obtained in FC after US and CC’s control group, respectively. The surface roughness of FC, IC, and CC was significantly affected by the application of various prophylaxis procedures (p < 0.05). AP and US+AP+RP presented the least and most affected surface roughness, respectively. The lowest surface gloss value was in the US and RP subgroups of FC. The process that the least reduced the surface gloss was AP. Material and procedure affected the color stability (p < 0.05) except for CC. The highest ΔE values were obtained in US+AP+RP subgroups. Indirect restorative materials showed less roughness and color change as well as higher gloss values after all periodontal prophylaxis procedures. The use of air-polishing has proven to be a reliable periodontal hygiene approach for direct and indirect restorations due to the less deterioration in the surface properties.