Aim: The aim of this systematic analysis was to assess the prevalence of dentinal microcracks at various levels (3, 6, and 9 mm from the apex) after using instruments made with conventional, R-Phase, and M-Wire NiTi alloys and the SAF system. Materials and Methods: Electronic searches were conducted in the databases Embase, Cochrane Library, Scopus, PubMed, and Web of Science. To arrange search methods, “MeSH” terms and/or keywords typically associated with the subject were paired with the Boolean operators “AND” and “OR.” Additional searches were conducted on the websites of four separate endodontic journals. After reading the titles and excluding duplicates, 1000 of the 1343 documents originally found were eliminated. Upon reviewing the abstracts, 310 of the remaining 343 experiments were also eliminated. Based on qualifying requirements, only 13 of the remaining 33 articles were included in the qualitative review. Results: All systems triggered dentinal microcracks; however, when chemo-mechanical preparation was performed using Self-Adjusting File (SAF) and systems manufactured with R-phase technology—K3XF and Twisted File Adaptive (TFA)—less of these defects were found when compared to those manufactured with traditional NiTi—ProTaper Universal and Mtwo—and with M-Wire—ProTaper Next, Reciproc, and WaveOne. Conclusions: A lower prevalence of dentinal microcracks was observed after using SAF and endodontic systems manufactured with R-phase.