Abstract Objectives Junior doctors are exposed to occupational and traumatic stressors, some of which are inherent to medicine. This can result in burnout, mental ill-health and suicide. Within a crossover pilot study comparing personalised, trauma-informed yoga to group-format exercise, qualitative interviews were conducted to understand the experience of junior doctors and whether such interventions were perceived to help manage these stressors. Methods Twenty-one doctors, 76% female, were order-randomised to consecutive 8-week yoga and exercise programmes. Fifty-two interviews were recorded before and after each programme. Results Many participants reported being time poor, sleep-affected, frequently stressed and occasionally in physical pain/distress. Major stressor themes were workplace incivility, death/human suffering and shift work with minimal support. Both interventions were acceptable for different reasons. Personalised yoga offered a therapeutic alliance, time to check-in and reduced anxiety/rumination. Group exercise provided energy and social connection. One participant found yoga beneficial following an acute workplace trauma: ‘It was really eye opening how much I felt my body just needed to detox … I wouldn't have gone to a group fitness the next day … I just wanted to relax and breathe …We still had a big debrief which was great … (but) I almost felt like … I dealt with it physically and emotionally before going into it (P20).’ Conclusion Junior doctors found both interventions useful for stress management adjunctive to other organisational programmes though for different and complementary reasons, possibly related to delivery mode. Personalised, trauma-informed yoga provided a confidential therapeutic alliance whereas group exercise offered social connection.