The aim of this study was to compare the occurrence of instrumentation and obturation related endodontic procedural mishaps following the use of either, stainless steel hand or engine-driven rotary instrumentation techniques. From a computerized hospital database, a total of 730 dental patient records who had received endodontic treatment by undergraduate dental students between August 2018 to September 2020 were retrieved. The inclusion criteria were primary (non-surgical) endodontic treatment on permanent teeth with complete radiographic records. Following record screening, a final sample of n = 475 dental records were included. Radiographic records were evaluated for both instrumentation and obturation related mishaps. The data was analysed using multiple logistic regression analysis (α = 0.05). Engine-driven rotary instrumentation resulted in a significant decrease in the overall occurrence of instrumentation related endodontic mishaps by 40% compared to hand instrumentation (Odds Ratio = 0.59 [0.36-0.97], p = 0.04). In particular, rotary instrumentation decreased ledge formation, perforation and obturation related mishaps, with minimal effect on the limitation of zipping. The use of rotary instrumentation techniques may reduce the incidence of instrumentation and obturation endodontic mishaps in the undergraduate dental clinic.