The objectives of this study were to evaluate how different disinfection protocols affect the surface roughness of gutta-percha (GP) cones used for the dental root canal filling using DIN 4768 standard and another alternative process for assessing roughness of small surface area (multiple profile), comparing both methods in order to identify similarities. The GP cones used were the conventional (C) and a new one impregnated with zirconia oxide, known as the coated cone (CC). Samples were distributed for each group and they were immersed in the correspondent chemical solution as follows: Group 1 (G1), sodium hypochlorite (NaOCl) at 5.25% for 1min; Group 2 (G2), sodium hypochlorite at 2.5% for 10min; and Group 3 (G3), chlorhexidine gluconate (CHX) at 2% for 5min, as recommended by dentistry protocols. The averages and standard deviations of the surface roughness parameters—average roughness (Ra) and root mean square deviation roughness (Rq)—were calculated. Statistical analysis was made before and after immersion by paired t-test. Results showed a statistically significant difference for C GP cones after immersion in 2% CHX and 2.5% NaOCl (p<0.01). No difference was found in CC GP cones. DIN 4768 standard and multiple profile measurements showed similar trends and behavior.