Chronic stress undermines psychological and physiological health. We tested three remotely delivered stress management interventions among clergy, accounting for intervention preferences. United Methodist clergy in North Carolina enrolled in a partially randomized, preference-based waitlist control trial. The interventions were: mindfulness-based stress reduction (MBSR), Daily Examen prayer practice, and Stress Proofing (stress inoculation plus breathing skills). Co-primary outcomes were symptoms of stress (Calgary Symptoms of Stress Inventory) and 48-hour ambulatory heart rate variability (HRV) at 12 weeks compared to waitlist control. Survey data were collected at 0, 12, and 24 weeks and 48-hour ambulatory HRV at 0 and 12 weeks. The 255 participants were 91% White and 48% female. Forty-nine participants (22%) without a preference were randomly assigned between the three interventions (n = 40) and waitlist control (n = 9). Two hundred six participants (78%) with a preference were randomly assigned to waitlist control (n = 62) or their preferred intervention (n = 144). Compared to waitlist control, MBSR [mean difference (MD) = −0.30, 95% CI: −0.41, −0.20; P < .001] and Stress Proofing (MD = −0.27, 95% CI: −0.40, −0.14; P < .001) participants had lower stress symptoms at 12 weeks; Daily Examen participants did not until 24 weeks (MD = −0.24, 95% CI: −0.41, −0.08). MBSR participants demonstrated improvement in HRV at 12 weeks (MD = +3.32 ms; 95% CI: 0.21, 6.44; P = .036). MBSR demonstrated robust improvement in self-reported and objective physical correlates of stress; Stress Proofing and Daily Examen resulted in improvements in self-reported correlates of stress. These brief practices were sustainable and beneficial for United Methodist clergy during the heightened stressors of the COVID pandemic. ClinicalTrials.gov identifier: NCT04625777.