Background The disinfection of dental impression materials is a cornerstone of infection control in dental practice. This study aimed to evaluate the effectiveness of two disinfectants, sodium hypochlorite and iodophor, on alginate and silicone impression materials, which are prone to microbial contamination. Methods The study was structured into two main groups based on the impression material: Group I (alginate) and Group II (addition silicone), each further subdivided into two subgroups for disinfection with sodium hypochlorite and iodophor. For each subgroup, initial microbial swabs were taken before any treatment, followed by a second swab after rinsing and a final swab after disinfection. The mean colony-forming unit (CFU) counts, standard deviations, and standard errors of the mean were calculated for each stage of treatment. Results Prior to disinfection, Group I had a mean CFU count of 2,529.40, while Group II had a lower mean CFU of 1,417.40. After rinsing, there was a significant decrease in CFUs in both groups, with Group I at 1,337.10 and Group II at 415.10. Post-disinfection, Group I showed a mean CFU count of 73.00 for sodium hypochlorite and 0.00 for iodophor. Similarly, Group II achieved a CFU reduction of 99.00 with sodium hypochlorite and 0.00 with iodophor, demonstrating a marked reduction in microbial presence. Conclusion Iodophor was exceptionally effective in disinfecting both alginate and silicone impression materials, eliminating all detectable CFUs. Sodium hypochlorite also significantly reduced microbial counts but was not as effective as iodophor. Rinsing prior to disinfection was instrumental in reducing the microbial load, underscoring its importance in the disinfection protocol.