Background The Royal Australasian College of Surgeons’ Board in General Surgery implemented Entrustable Professional Activities (EPAs) in its competency-based training program in 2022. This qualitative study explored trainee perceptions and experiences of EPAs in their general surgical training in Australia. Methodology Six first-year general surgery trainees were recruited to participate in semi-structured interviews. The interviews explored the trainees’ experiences of EPAs, their perceptions of the effect on their independence in completing clinical activities and on patient safety, and their suggestions for how to improve EPA implementation in training. Initial inductive data analysis was followed by modified narrative analysis. Results The findings suggest that trainees regard EPAs as a potentially useful tool for assessing their competence. However, the study also found that EPAs can be challenging for trainees, particularly in terms of the level of self-regulation and independence required, lack of engagement by trainers, sub-optimal feedback, and the high number of repetitive assessments. These challenges negatively impacted trainee motivation to complete EPA assessments in the required timeframes. Suggestions for improved implementation related directly to overcoming identified challenges. Conclusion Implementing EPAs in general surgery training has some positive benefits for trainees, although these may be currently offset by challenges in achieving optimal use for this assessment form. Further research and evaluation is required for quality improvement in implementing and using EPAs in surgical training.