The present study aimed to investigate the effects of different obturation techniques on the main and accessory canal filling quality of a premixed calcium silicate endodontic sealer (Endoseal TCS). We also highlighted the validity of the methods used for evaluating the canal filling quality. Thirty single-rooted premolars were used for the main canal filling and 75 were used for accessory canal filling. The canals were instrumented and randomly divided into three groups according to the filling techniques: (1) single-cone technique (SC), (2) single-cone with ultrasonic activation (SU), and (3) warm vertical compaction (WV). Voids in relation to the root canal fillings were assessed using cross-section images from microcomputed tomography (μCT) scans or transversely sectioned tooth specimens (n = 10). After demineralization and clearing of the teeth, the incidence, number, and completeness of the accessory canal fillings were evaluated (n = 25). One-way analysis of variance (ANOVA) and Tukey’s post hoc test was used for the evaluation of the voids in the main root canal and the incidence and number of filled accessory canals. Pearson’s chi-squared (χ2) test was used for the evaluation of the filling completeness (α = 0.05). In the stereomicroscopic evaluation of the sectioned specimen, the SC group had significantly higher void occurrence than the other groups (p < 0.05), although there was no difference between groups in the μCT evaluation. However, there was no difference between the SU and WV. There was no difference between all the groups regarding the incidence, number, and completeness of the accessory canal fillings. When the premixed calcium silicate sealer is used with SC, the ultrasonic activation is recommended to obtain a better main canal filling quality. In contrast, the obturation techniques did not affect the accessory canal filling. We also recommend using the sectioning method when the void formation in the root canal filling materials is evaluated.