This study aims to compare the shaping efficiency of the nickel–titanium instrument systems, One Reci and ProTaper Ultimate, using micro-CT (micro-computed tomography) in traditional and conservative endodontic access cavities. The experimental groups were formed according to the type of access cavity and Ni–Ti file system to be used. Sixty mandibular molar teeth were randomly divided into two main groups, the conservative access cavity (CAC) group and the traditional access cavity (TAC) group, and randomly divided into two subgroups according to the file system. The groups were compared with a two-way ANOVA analysis in terms of volume change, surface area, non-instrumented area transportation, and thickness of the dentin in the danger zone area after root canal preparation. The groups showed no statistically significant differences in terms of volume change, surface area, or the thickness of the dentin in the danger zone area after root canal preparation (p > 0.05). However, in the percentage of non-instrumented areas post-instrumentation between groups, the percentage of non-instrumented areas was statistically higher in specimens with CAC compared to TAC (p < 0.05). Canal transportation was higher in CAC at all distances from the apical region (p < 0.05). Within the limitations of this study, CAC can also be used with some precautions as an alternative to TAC.