Atomic force microscope (AFM) is a well-established methodology for structural characterization of materials. The purpose of this study was to investigate the effects of sodium hypochlorite (NaOCl) solutions on gutta-percha cone structure using AFM. Three standardized gutta-percha cones were cut 3 mm from the tip, attached to a glass base and immersed in 0.5, 2.5, or 5.25% NaOCl solutions. After 1 and 5 min the samples were positioned in the atomic force microscope. The analyses were performed on twelve different points ( n = 12) located between 1 and 2 mm from the tip after each period of immersion in NaOCl. Gutta-percha cone without any NaOCl treatment were used as control. Root mean square (RMS) parameters for contact mode imaging and force modulation microscopy variations were measured. The differences between RMS values were tested by ANOVA with Fisher’s protected LSD test for multiple comparisons (p < 0.05). Aggressive deteriorative effects on gutta-percha cone elasticity were observed for 5.25% NaOCl at 1 min when compared to the control (p < 0.05). In addition, 2.5% and 5.25% NaOCl solutions caused topographic changes after 5 min when compared to the control (p < 0.05). Conversely, 0.5% NaOCl solution did not cause any alteration on topography or elasticity of gutta-percha cone structure when compared to the control (p < 0.05). Thus, 0.5% NaOCl solution is a safe alternative for rapid decontamination of gutta-percha cones.