Health professionals are among the most vulnerable to work stress and emotional exhaustion problems. These health professionals include tutors and resident intern specialists, due to the growing demand for the former and the high work overload of the latter. Mindfulness training programs can support these professionals during times of crisis, such as the current global pandemic caused by the coronavirus-19 disease. The objective of this study was to compare the effectiveness of an abbreviated Mindfulness-Based Stress Reduction (MBSR) and Mindful Self-Compassion (MSC) training program in relation to a standard training program on the levels of mindfulness, self-compassion, and self-perceived empathy in tutors and resident intern specialists of Family and Community Medicine and Nursing. A total of 112 professionals attached to six Spanish National Health System teaching units (TUs) participated in this randomized and controlled clinical trial. Experimental Group (GE) participants were included in the standard or abbreviated MBSR programs. The Five Facet Mindfulness Questionnaire (FFMQ), the Self-Compassion Scale short form (SCS-SF), and the Jefferson Scale of Physician Empathy (JSPE) were administered three times during the study: before, immediately after, and 3 months after the intervention. Adjusted covariance analysis (ANCOVA), using pretest scores as the covariate, showed a significant increase in mindfulness (F(2,91) = 3.271; p = 0.042; η2 = 0.067) and self-compassion (F(2,91) = 6.046; p = 0.003; η2 = 0.117) in the post-test visit, and in self-compassion (F(2,79) = 3.880; p = 0.025; η2 = 0.089) in the follow-up visit, attributable to the implementation of the standard training program. The standard MBSR and MSC training program improves levels of mindfulness and self-compassion, and promotes long-lasting effects in tutors and resident intern specialists. New studies are needed to demonstrate the effectiveness of abbreviated training programs.