The present study evaluated the quality of single-cone root canal fillings with bioceramic (BC) sealer using three different techniques by means of micro-computed tomography (micro-CT). The canals of 30 extracted single-rooted permanent teeth were shaped with R40 Reciproc blue files and filled with the single-cone technique (SCT). BioRoot RCS BC sealer was placed inside the canals with one of the following master cones: R40 cone to working length (RWL, n = 10); R40 cone trimmed 1 mm short of working length (RWL-1, n = 10); non-standardized gutta-percha cone to working length (NSWL, n = 10). A quantitative and qualitative micro-CT analysis assessed the filling quality and internal/external voids formation. Collected data underwent statistical analysis by multivariate one-way analysis of variance (α = 0.05). In all groups, the voids were minimal and prevalently external. The NSWL and RWL-1 groups had increased sealer ratios in the whole canal and the apical canal portion, respectively. The lowest amounts of voids were found in the RWL group; the void volumes were slightly greater in the RWL-1 mm and NSWL groups, especially at the apical level. Two alternative SCTs showed satisfactory filling ability, uniform distribution of the BC sealer, and a minimally increased voids formation compared to the standard SCT with dedicated cone. The two tested alternative SCTs could take advantage of the beneficial characteristics of the BC sealer, which evenly filled the endodontic space, ideally sealing both the major and the accessory communications with the periodontium.