Previous research links contemplative practices, such as meditation, with stress reduction. However, little is known about the psychological mechanisms underlying this relationship. This study compares the physiological stress response (reactivity and recovery) measured by changes in salivary cortisol, heart rate, heart rate variability, and the associated stress-related ratings in long-term meditation practitioners (N = 29) and age- and sex- matched meditation naïve controls (N = 26). The participants were administered the Trier Social Stress Test in its active and placebo versions. The results demonstrated that long-term meditation practitioners had faster cortisol recovery from stress, and experienced less shame and higher self-esteem after the exposure to social-evaluative threat. In addition, long-term meditation practitioners scored higher on adaptive cognitive emotion regulation strategies, such as acceptance and positive reappraisal, and lower on maladaptive ones, such as catastrophizing. The cognitive emotion regulation strategy of acceptance mediated the relationship between meditation practice and cortisol recovery. These results suggest that meditation practice is associated with faster recovery from stress due to the employment of adaptive emotion regulation strategy of acceptance, delineating a pathway underlying the positive effects of meditation on stress.