Introduction: After endodontic surgery, radiographic assessment is the method of choice to monitor bone defect healing. Cone-beam computed tomography scans are useful to check and identify the reasons of failure of surgical intervention or confirm healing; however, the artifact generated by some root-end filling material might compromise this task. The objective of the study was to compare the amount of artifacts generated by 4 root-end filling materials and to test multiple exposure settings used with these materials, when the effective dose generated by each protocol was taken into consideration. Methods: Twenty central incisors were endodontically treated with retrograde obturation by using amalgam, Biodentine, MTA, and Super-EBA (5 of each). They were placed in a skull with soft tissue simulation and scanned by using the Planmeca Promax Max with different kilovolt peaks (kVp): 66, 76, 84, and 96 with and without the use of metal artifact reduction (MAR) algorithm and with low, normal, and high resolution and high definition. The Dose Area Product was registered, and the effective dose was calculated. Results: Amalgam generated the highest amount of artifacts, whereas MAR and low resolution created fewer artifacts than other settings. The artifacts were also reduced with 96 kVp. The effective dose calculated with low resolution was remarkably lower than other resolutions. Conclusions: When used as root-end filling material, Biodentine, MTA, and Super-EBA generated fewer artifacts than amalgam. The use of 96 kVp with MAR and low resolution also reduced artifacts on the image and at the same time generated the lowest effective dose.