The aim of this study was to evaluate alterations on the surface of gutta-percha and Resilon cones when exposed to 2% chlorhexidine gel (CHX) and 5.25% sodium hypochlorite (NaOCl) and to evaluate their possible antibacterial residual effects against Enterococcus faecalis and Porphyromonas gingivalis. A total of 270 medium tapered cones (135 gutta-percha and 135 Resilon) were selected and divided into three groups, according to the substance (NaOCl, CHX, and sterile saline solution). The cones were immersed in each substance (for 1, 5, 10, 20, and 30 min), rinsed in saline solution, and dried. They were placed onto inoculated agar plates and incubated under specific conditions. Scanning electron microscopy analysis was performed on additional 270 disinfected cones. Another 18 cones were used as controls. Based on the results, it was concluded that Resilon cones exposed to CHX for 10, 20, and 30 min demonstrated residual antibacterial action and that substances did not cause alterations to the cones' surface.