Well-being activities may help to counteract physician burnout. Yoga is known to enhance well-being, but there are few studies of yoga as an intervention for physicians in training. This prospective methodology-development study aimed to explore how to establish a yoga-based well-being intervention for physician trainees in a large urban training hospital. We aimed to identify factors that contribute to trainee participation and explore an instrument to measure changes in self-reported well-being after yoga. Cohorts included a required-attendance group, a voluntary-attendance group, and an unassigned walk-in yoga group. Weekly 1-hour yoga sessions were led by a qualified yoga instructor for 4 weeks. The seven-question Resident Physician Well-Being Index (RPWBI) was used to measure resident well-being before yoga, after 4 weeks of yoga, and 6 months post-yoga. Trainees attending each session ranged from 17 for required yoga to 0–2 for voluntary yoga, 2–9 for lunchtime walk-in yoga, and 1–7 for evening walk-in yoga. In the required-yoga group (n = 17), overall RPWBI mean scores did not change significantly across the three query times, and participation in the survey declined over time. The mean baseline RPWBI score for the required group before yoga was in the non-distressed range and answers to the seven individual questions varied. Requiring a yoga activity for medical trainees may be a good strategy for promoting participation in yoga. The RPWBI may have limited utility for measuring changes in overall group well-being after a yoga intervention.