This study compared the effects of different final irrigation protocols on the mechanical properties and structural integrity of root dentine. One-hundred eight teeth were instrumented and irrigated with sodium hypochlorite (NaOCl) using conventional irrigation (CI). Teeth were distributed into four groups based on final irrigation protocols: Control Group (CG): 17%EDTA/CI + H2O; G1: 2.5%NaOCl/Passive Ultrasonic Irrigation (PUI) + EDTA/PUI + NaOCl/PUI (60s each); G2: EDTA/PUI + NaOCl/PUI (30s each); G3: EDTA/PUI + NaOCl/PUI + H2O/PUI + CHX/PUI (30s each). Four tests were conducted: three-point flexural strength test, Scanning Electron Microscopy analysis, microhardness assessment, and the push-out bond strength (POBS) of the filling material to the root dentine. Data were analyzed using ANOVA and Tukey tests (Flexural strength), and Student t-test (Microhardness). Erosion scores and POBS were analyzed by Kruskal-Wallis and Dunn tests (α = 0.05). Results indicated no significant differences in flexural strength (p > 0.05) among groups. CG exhibited the lowest erosion scores in the cervical third. In the middle third, CG had lower scores than G1 and G2, while in the apical third, CG had lower scores than G1 (p < 0.05). Microhardness values decreased following the protocols (p < 0.05), except for the CG (p > 0.05). G2 displayed higher POBS values in the middle and apical thirds (p < 0.05). The protocols did not significantly influence the flexural strength of root dentine. However, they did affect microhardness and promoted greater erosion. The best results for POBS were observed when the final irrigation involved the sequential use of EDTA and NaOCl employing PUI for 30 seconds in each solution.