Doctoral students experience high rates of mental health distress and dropout; however, the mental health and wellness of engineering doctoral students is understudied. Studies of student persistence, wellness, and success often aggregate fields together, such as by studying all engineering students. Thus, little work has considered the experiences of biomedical engineering (BME) doctoral students, despite differences between doctoral BME research, course content, and career expectations compared with other engineering disciplines. In this qualitative interview case study, we explore stressors present in the BME graduate experience that are unique from engineering students in other disciplines. We analyzed a longitudinal interview study of doctoral engineering students across four timepoints within a single academic year, consisting of a subsample (n = 6) of doctoral students in a BME discipline, among a larger sample of engineering doctoral students (N = 55). BME students in the sample experienced some themes generated from a larger thematic analysis differently compared with other engineering disciplines. These differences are presented and discussed, grounded in a model of workplace stress. BME participants working in labs with biological samples expressed a lack of control over the timing and availability of materials for their research projects. BME participants also had more industry-focused career plans and described more commonly coming to BME graduate studies from other fields (e.g., another engineering major) and struggling with the scope and content of their introductory coursework. A common throughline for the stressors was the impact of the interdisciplinary nature of BME programs, to a greater extent compared with other engineering student experiences in our sample. We motivate changes for researchers, instructors, and policymakers which specifically target BME students and emphasize the importance of considering studies at various unit levels (university department level vs college level vs full institution) when considering interventions targeting student stress and wellness.