Aim: The aim of this study was to investigate the influence of cleaning methods to remove zinc oxide-eugenol-based root canal sealer (Endomethasone) on the bond strength of the self-etching adhesive to dentin. Materials and Methods: Twenty crowns of bovine incisors were cut to expose the pulp chamber. A zinc oxide- and eugenol-based sealer was placed for 10 min in contact with the pulp chamber dentin. Specimens were divided into four groups according to the cleaning method of dentin used: G1, no root canal sealer (control); G2, 0.9% sodium chlorite (NaCl); G3, ethanol; and G4, followed by diamond drill. After cleaning, the teeth were restored with composite resin and Clearfil SE Bond. All specimens were sectioned to produce rectangular sticks and dentin/resin interface was submitted to microtensile bond testing. The mean bond strengths were analyzed using ANOVA/Tukey (α = 0.05). Results: G3 and G4 showed bond strengths similar to the G1 (P > 0.05). A significant decrease in the bond strength in the G2 was observed (P < 0.05). G1, G3, and G4, the predominant failure mode was the mixed type. The prevalence of adhesive failure mode was verified in the G2. Conclusion: The cleaning methods affected the bond strength of the self-etching adhesive to dentin differently.