This research study aimed to investigate the impact of probiotic mouthwash and kefir on the surface characteristics, specifically surface roughness and microhardness, of different restorative materials, as well as permanent and deciduous tooth enamels. Thirty disc-shaped specimens were prepared from composite resin (G-ænial Posterior (GP)), polyacid-modified composite resin (compomer) (Dyract-XP (DXP)), and resin-modified glass ionomer cement (Ionoseal (IS)). Additionally, thirty specimens of enamel were obtained from permanent teeth (PT) and thirty from deciduous teeth (DT) by embedding buccal and lingual sections, acquired through vertical sectioning of 15 permanent and 15 deciduous human tooth crowns in the mesiodistal orientation within acrylic resin blocks. The specimens were then categorized into three distinct groups and immersed for 14 days in one of the following solutions: distilled water, kefir or probiotic mouthwash. The mean surface roughness values of all specimens were assessed using an atomic force microscope, while the mean surface microhardness was measured using a Vickers hardness measuring instrument. The results revealed a statistically significant difference in mean surface roughness among the various restorative materials ( < 0.001). Among the restorative materials, the IS material exhibited notably higher mean surface roughness values than other restorative materials and tooth enamel, while no significant differences were observed between the PT and DT groups. Importantly, the main effect of the solutions under investigation was not statistically significant ( = 0.208). No significant difference was found between the surface roughness values of specimens subjected to the different solutions. When evaluating the effects of materials and solutions on microhardness, the main effects of material and solution variables and the influence of material-solution interactions were statistically significant ( < 0.001). Taken together, these results indicate that consistent use of kefir or probiotic mouthwashes may impact the surface properties of various restorative materials and tooth enamel.