This study analysed the bioceramic sealer cleaning ability of two chemo-mechanical systems in intact and restored teeth. Thirty-two single-rooted teeth were used, and half of them restored with a pre-endodontic composite restoration (PCR). All samples were instrumented with a size 40 Reciproc Blue file and filled with BioRoot RCS. Canals were retreated using the R40 and then R50 Reciproc Blue. The samples were divided into four experimental groups (n = 8): intact teeth/passive ultrasonic irrigation (PUI) (G1), intact teeth/shock wave-enhanced emission photoacoustic streaming (SWEEPS) (G2), PCR/PUI (G3) and PCR/SWEEPS (G4). The samples were scanned by micro-CT before and after retreatment, and the volume of remaining filling material was evaluated. The minor percentage of residues were observed in G2, with a volume of 0.447 ± 0.356% of the endodontic space (P < 0.001). The Reciproc/SWEEPS technique showed the better performance in intact teeth compared with PUI technique. Pre-endodontic restoration did not significantly affect the effectiveness of sealer removal.