This study aimed to evaluate Olea europaea (olive) leaves and Morus nigra (black mulberry) leaves as potential natural alternatives to sodium hypochlorite (NaOCl) endodontic irrigant. Their antimicrobial activity against Enterococcus faecalis (E. faecalis) and their effects on both root dentin microhardness and push-out bond strength of resin sealer/root dentin were assessed. Fifty-four extracted teeth were selected. Samples were grouped according to the irrigant used: group I (control): 2.5% NaOCl, group II: 8% ethanolic extract of Olea europaea, and group III: 2% ethanolic extract of Morus nigra. Antibacterial activity (n = 6) was evaluated after each canal was autoclaved, inoculated with E. faecalis, and incubated. Canals were sampled before and after chemicomechanical canal preparation with 2 mL of irrigant. The colony-forming units (CFUs) were counted at 1/10 and 1/100 broth concentrations. Vickers hardness number (VHN) of root dentin (n = 6) was measured before and after root canal preparation and irrigation. Push-out bond strength testing (n = 9) was carried out following preparation, irrigation, obturation, and thermocycling. Results were considered statistically significant at p ≤0.05. Following irrigation, the CFUs of E. faecalis were significantly reduced with no significant difference in the CFU count between all groups at both broth concentrations. A significant reduction in root dentin microhardness resulted in all groups following irrigation, with Morus nigra resulting in the lowest percentage reduction (26.42 ± 1.12). The lowest significant mean push-out bond strength was revealed in the Olea europaea group (3.372 ± 1.513 MPa). The use of 2% mulberry (Morus nigra) leaf extract and 8% olive (Olea europaea) leaf extract as alternatives to NaOCl provides promising antimicrobial action against E. faecalis. 2% Morus nigra extract may represent a promising natural endodontic irrigant.