Aim The aim of the present study was to investigate bacterial leakage and marginal adaptation of bioceramic apical plugs. Methods Extracted human mandibular premolars were prepared to simulate open apex using No. 4 Peeso reamer in retrograde direction. In total, 150 specimens were divided into 10 groups by obturation with five bioceramics in two thicknesses. Groups 1, 3, 5, 7, and 9 were obturated with ProRootMTA, Biodentine, TotalFill BC RRM paste, TotalFill BC RRM putty, and RetroMTA at 3 mm, and groups 2, 4, 6, 8, and 10 were obturated with the same materials at 4 mm. Ten specimens in each group were evaluated for bacterial leakage of Enterococcus faecalis for 75 days. Five specimens from each group were sectioned to investigate the gap area under scanning electron microscope. Results The 3‐ and 4‐mm Biodentine and TotalFill BC RRM putty groups and the 4‐mm ProRootMTA group exhibited less bacterial leakage and lower mean percentage of gap area than those of the other groups. TotalFill BC RRM paste showed the highest leakage for both the 3‐ and 4‐mm groups. Conclusion The 3‐ and 4‐mm Biodentine and TotalFill BC RRM putty groups and the 4‐mm ProRootMTA group exhibited the best sealing ability and marginal adaptation of apical plugs.