<p>In cases where initial root canal therapy is unsuccessful, retreatment is the first treatment choice. However, when bioceramic-based sealers have been used in the initial treatment, their complete removal can be challenging. The objective of this study was to evaluate the efficacy of three final irrigation activation methods-conventional needle irrigation, passive ultrasonic activation, and EDDY activation—using a scanning electronic microscopy (SEM) to evaluate the removal of bioceramic-based sealers after retreatment. A total of 108 single-rooted teeth were prepared using ProTaper Next rotary files. The samples were obturated with either MTAFillapex or BioSerra (<i>n</i> = 54) and stored for 2&#xa0;weeks post-obturation. After the retreatment procedures, the teeth were divided into six groups (<i>n</i> = 18 per group) based on final irrigation activation method used. Group1:MTAFillapex-CNI, Group2:BioSerra-CNI, Group3:MTAFillapex-EDDY, Group4:Bioserra-EDDY, Group5:MTAFillapex-UltraX, Group6:Bioserra-UltraX. The roots were sectioned longitudinally, and the coronal, middle and apical parts were investigated under a SEM. The data were then statistically analysed. The EDDY activation technique proved significantly more effective in removing MTA Fillapex across all sections of the root canal (<i>p</i> &lt; 0.001). In contrast, Ultra-X was more effective in removing Bioserra in the middle and apical sections (<i>p</i> = 0.003, <i>p</i> &lt; 0.001). These findings suggest that activation procedures may be preferable for removing bioceramic-based root canal sealer.</p>