Objective Endoscopic ear surgery is gaining popularity as a minimally invasive surgical technique for middle ear diseases. Its ongoing implementation into clinical routine has consequences regarding teaching of middle ear anatomy and surgery. To improve undergraduate and postgraduate training, we investigated the perception of and preference for endoscopy as compared with microscopy at different educational levels. Study Design Qualitative study based on a thematic analysis approach. Setting Tertiary academic medical center. Methods After a standardized curriculum was run on endoscopic and microscopic anatomy and surgical skills education, 5 focus groups were held. The interviews were conducted, video recorded, transcribed, and analyzed. Analysis of the data gave rise to 11 themes showing the participants’ perceptions and preferences. Results Five medical students, 11 otorhinolaryngology residents, and 3 staff members participated in this qualitative study. For anatomy teaching, there was a clear preference for the endoscopic technique. The main advantages were the enhanced overview and perception of the anatomic details provided through endoscopy. For skills acquisition, the perceived advantages of the techniques were the same view of the surgical field for endoscopy and the 2-handed surgical technique for microscopy. However, there was no clear preference between the techniques for skills acquisition. Conclusion The endoscopic technique was generally judged more beneficial for teaching anatomy, especially due to the greater visualization of the complex middle ear anatomy. Given that both techniques will remain important to future surgeons, the relative unique benefits of each must be considered when designing and optimizing curricula for otologic education.