Surface attributes of a restoration play an important role in adherence of plaque bacteria. Prophylaxis methods may be involved in modification of or damaging the restoration surface. The aim of the present study was to evaluate the effect of two prophylaxis methods on adherence of Streptococcus mutans to the surface of two restorative materials. A total of 60 specimens were prepared from each material; a microfilled composite resin (HelioProgress) and a giomer (Beautifil II). For each material, the specimens were randomly divided into three groups (n=20). Group 1: no prophylaxis treatment (control); Group 2: prophylaxis with pumice and rubber cup; Group 3: prophylaxis with air-powder polishing device (APD). The surfaces of selected specimens from each group were evaluated under a scanning electron microscope (SEM), and the surface topography formed by the two prophylaxis methods was determined by atomic force microscopy (AFM). Adherence of Streptococcus mutans to the surface of specimens was determined by the plate counting method following immersion in a bacterial innoculum for 4 hours, rinsing and sonication. Data were analyzed by two-way ANOVA and post hoc Tukey test for multiple comparisons. Statistical significance was set at P<0.05. Bacterial adherence was significantly affected by both factors: restorative material type and prophylaxis method (P<0.0005). Mean bacterial adhesion was significantly higher in composite groups compared to corresponding giomer groups. Within each material, bacterial adherence was significantly lower in the control group compared to prophylaxis groups. Prophylaxis with pumice and rubber cup resulted in a significantly lower bacterial adherence compared to prophylaxis with APD. Based on the results of the present study, giomer specimens demonstrated lower bacterial adherence compared to composite resin specimens. In both materials, the highest bacterial adherence was observed with prophylaxis with APD, pumice and rubber cup and the control group, respectively.