Structured Abstract Objective The aim of this study was to evaluate the effects of superelastic nickel‐titanium (SE NiTi), copper‐nickel‐titanium (CuNiTi) and titanium‐molybdenum alloy (TMA) archwires with different surface properties on dental plaque retention and microbial colonization. Setting and Sample Population Totally 25 individuals, consisting of 16 girls and nine boys with mean age of 15.69 ± 1.70, were included in this study. Material and Methods The effects of the SE NiTi, CuNiTi and TMA archwires with different surface properties on the amount of Streptoccocus sp and Lactobacillus sp were investigated with three different parameters including clinical periodontal indexes, microbial swab and archwire samples. Phenotypic isolation was performed from microbial swab and archwire samples using culture method; genotypic isolations were performed by the polymerase chain reaction method. Results There was no statistically significant difference between SE NiTi, CuNiTi and TMA archwires in terms of periodontal parameters (P > .05). When microbial swabs and archwires samples from different archwire groups were evaluated by culture method, no statistically significant difference was found between the groups (P > .05). A statistically significant difference was found between the amount of Lactobacillus sp in the swab samples of the CuNiTi archwire after the purification period (P = .023). S mutans were found to be more quantity than other bacterial types in all archwires. Conclusion The amount of microbial involvement was found to be lower in CuNiTi archwires than in the post‐purification period. This may be due to the antimicrobial effect of copper.