We aimed to evaluate the effect of varying the tube current and the Metal Artifact Reduction (MAR) tool on the detection of the missing second mesiobuccal (MB2) canal. Forty maxillary molars (20 with and 20 without MB2) were selected and confirmed by micro-CT. The teeth underwent endodontic preparation, with the canals filled using gutta-percha and a silver-palladium metal post. CBCT scans were acquired using the OP300 Maxio system (voxel size: 0.085 mm, FOV: 50 x 50 mm) at 4 mA, 6.3 mA, and 12.5 mA, with and without MAR activation. The areas under the receiver operating characteristic curves (AUCs), sensitivities, and specificities were calculated for five examiners and compared using two-way ANOVA (p < 0.05). Intra- and interexaminer agreements were assessed using the weighted Kappa test. The AUC values ranged from 0.90 to 0.94, sensitivity from 0.75 to 0.78, and specificity from 0.89 to 0.95. Intra- and interexaminer indices ranged from moderate to substancial. Based on the tube current settings or MAR activation, there were no significant differences in the MB2 canal detection. Therefore, varying the tube current and MAR tool activation did not affect MB2 canal detection, with values close to 4 mA without MAR activation recommended in this scenario to reflect a better dose-benefit ratio.