Background: Molar root canal treatment (RCT) is challenging and requires training and specific skills. Rotary instrumentation (RI) reduces the time needed for instrumentation but may increase the risk of certain procedural errors. The aims of this study were to evaluate the quality of molar RCTs provided by undergraduate students, to compare the prevalence of procedural errors following manual and RI, and to assess the students’ self-perceived confidence to perform molar RCT without supervision and their preference for either manual or RI. Methods: Molar RCTs performed by the final year students were evaluated radiographically according to predefined criteria (Appendix 1). The procedural errors, treatment details, and the students’ self-perceived confidence to perform molar RCT and their preference for either manual or RI were recorded. Descriptive statistics were performed, and the Chi-squared test was used to detect any statistically significant differences. Results: 60.4% of RCTs were insufficient. RI resulted in more sufficient treatments compared with MI (49% vs. 30.3% respectively. X²: 7.39, p = 0.007), required fewer visits to complete (2.9 vs. 4.6 respectively. X²: 67.23, p < 0.001) and was the preferred technique by 93.1% of students. The most common procedural errors were underextension of the root canal obturation (48.4%), insufficient obturation (45.5%), and improper coronal seal (35.2%) without a significant difference between the two techniques. 26.4% of the participating students reported that they did not feel confident to perform molar RCT without supervision. Conclusion: The quality of molar RCT provided by UG students was generally insufficient. RI partially improved the technical quality of RCT compared with MI. UG students need further endodontic training and experience before they can safely and confidently practise molar RCT.