Aim: The research's aim was to evaluate the effects of four different rotary nickel-titanium (NiTi) endodontic file systems on the ability to alter the root canal space volume, generation of apical transportation, and file-centering ability using micro-CT imaging. Materials and Methods: A total of 40 extracted mandibular premolars with straight-root canals were selected and instrumented using four NiTi rotary file systems namely ProTaper Next™ (PTN), ProTaper Gold™ (PTG), WaveOne® Gold (WOG), and Reciproc® Blue (RCB). Results: The Kruskal-Wallis H test revealed no statistically significant differences in canal transportation at the 1 mm [H (3) = 6.22, p = 0.891], 3 mm [H (4) = 1.724], and 5 mm locations among the four tested instruments. Although all file systems contributed to some degree of canal transportation, PTN, and PTG did so to the least extent. The optimum file-centering efficiency was demonstrated by PTN and WOG, while PTG and RCB showed the least. Conclusion: This study revealed that all tested files caused an increase in root canal volume and exhibited a tendency for apical transportation due to their inability to remain centered within the canal during preparation.