Moenkhaus established the graduate training program leading to the PhD in physiology at IU School of Medicine, because he was determined to train scientists as well as medical students. Moenkhaus single-handedly undertook the task of fostering a program of graduate physiological research at IU School of Medicine until 1922. He was also a one-person team for teaching medical physiology, while managing to supervise 13 masters and 2 doctoral degree recipients.
A notable student was Sid Robinson, who was inspired and to pioneer an exercise physiology course and, ultimately, became a physiology faculty member and leader in the field. Moenkhaus retired July 1941 as professor emeritus. To commemorate his passion for graduate training, he dedicated to the Department of Physiology the funding for a pre-doctoral fellowship of $24,500 based on academic performance.