Aim To assess the impact of conservative endodontic access cavities (CEC) and truss access cavities (TAC) during root canal treatment performed on mandibular molars in terms of: ability to shape and fill root canals, microbial reduction in canals, and cleaning of the pulp chamber. In addition, the fracture resistance of the teeth after coronal restoration was assessed. Traditional endodontic cavities (TEC) were used as a reference technique for comparison. Methodology Thirty extracted intact mandibular molars were scanned in a microcomputed tomography device (micro‐CT), matched based on similar anatomical features and assigned to TEC, CEC or TAC groups (n = 10). The specimens were accessed accordingly, and root canals were contaminated with bacterial suspensions of Enterococcus faecalis (21 days). Subsequently, the first microbial sample was collected from root canals (S1). The canals were initially prepared with Reciproc Blue R25 instrument followed by a second instrumentation using Reciproc Blue R40. Eight mL of 0.5% NaOCl were used as an irrigant for each instrument. A final irrigation protocol was performed with 2 mL of 0.5% NaOCl, 2 mL of 17% EDTA and another 2 mL of 0.5% NaOCl. Microbial samples were collected from root canals after R25 (S2), R40 (S3) and final irrigation (S4). The teeth were rescanned after S4. Then, root canals were filled, rescanned, restored and the teeth subjected to fracture resistance tests. The statistical analysis was performed with type I negative binomial and beta 0‐1 inflation regression models for microbiological analysis. Instrumentation, filling and resistance to fracture results were subjected to anova and Tukey tests (P < 0.05). Results S4 revealed no significant variations in microbial reduction amongst the groups (P > 0.05). TEC had a significantly lower percentage of unprepared surface area than CEC (P < 0.05). No differences were found regarding the percentage of dentine removed, transportation, centring ability and filling voids amongst the groups (P > 0.05). The TEC group had a significantly lower volume of remaining root filling material within the pulp chamber than CEC and TAC groups (P < 0.05). There was no difference regarding fracture resistance amongst the groups (P > 0.05). Conclusion Conservative access cavities did not offer any advantage in comparison with the traditional endodontic cavities in any of the parameters considered. Furthermore, conservative methods were associated with larger percentages of unprepared canal surface area and larger volumes of remaining root filling material within the pulp chamber.