The aim of this in vitro study was to compare the apical sealing ability of total fill bioceramic root repair material (BC-RRM) and mineral trioxide aggregate (MTA), regarding the retrograde preparation technique used: ultrasonic or erbium, chromium: yttrium, scandium, gallium, or garnet (Er,Cr:YSGG) laser. The study sample consisted of 48 human single-rooted teeth. After root-end resection, the samples were divided into two groups, according to the retrograde preparation technique used: Group 1: ultrasonic; Group 2: Er,Cr:YSGG laser. In each group, half of the retrograde cavities were filled with BC-RRM, and the other half were filled with MTA. The specimens were mounted in tubes and sterilized in plasma. The root canals were inoculated with Enterococcus faecalis, and the tubes were filled with fetal bovine serum, leaving the apical part of the root in the serum. After 30 days, the canals were sampled and cultured, and the colony forming units (CFUs) were counted with the additional polymerase chain reaction (PCR analysis). There was no significant difference between ultrasonic groups and the Er,Cr:YSGG-MTA group, regarding the number of CFUs (p > 0.05). The Er,Cr:YSGG-BC-RRM group showed the highest number of remaining viable bacteria (p < 0.001). Both filling materials filled in ultrasonic preparations presented similar sealing abilities. The BC-RRM showed more leakage when used in retro cavities prepared with the Er,Cr:YSGG laser.