College students experienced increased stress and anxiety during the COVID‐19 pandemic. This study evaluated the effect of brief online Isha Upa Yoga modules on undergraduates' mental health and well‐being. Randomized control trial (RCT) with waitlist control crossover (N = 679). The intervention group was instructed to learn and practice the modules daily for 12 weeks. At the end of the 4‐week RCT, the control group was instructed to learn and practice the modules for the remaining 8 weeks. Primary outcomes included stress and well‐being. Secondary outcomes included anxiety, depression, resilience, positive affect and negative affect. Linear mixed‐effects models were used for analyses. Isha Upa Yoga significantly reduced stress (Group [intervention, control] × Time [baseline, Week 4] interaction, p = .009, d = .27) and increased well‐being (Group × Time interaction p = .002, d = .32). By the study's end, the intervention and control groups experienced significant improvements in well‐being (p < .001, p < .001), stress (p < .001, p < .001), anxiety (p < .001, p < .001), depression (p < .001, p = .004), positive affect (p = .04, p < .001), and negative affect (p < .001, p < .001). Online Isha Upa Yoga shows promise for mitigating the pandemic's negative impact on undergraduates' mental health and improving their well‐being.