In the last two decades, formalized social-emotional learning (SEL) programs in schools have proliferated in response to a staggering increase in mental, social, and emotional challenges for youth. SEL programs differ in their theoretical foundations, though there are commonalities among them. Self-regulation (SR) surfaces as an important pillar. Researchers have relied mostly on self-reporting and teacher questionnaires to measure the effectiveness of these programs to improve SR and other aspects of youth well-being, without explicitly considering the physiological effects of these interventions on the biomarkers of youth. By addressing this gap, program researchers, developers, and educators can reach their stated objectives more effectively, thereby better nurturing SR and other social-emotional competencies. This paper explores a new model and rationale for incorporating physiological metrics (biomarkers), such as vagal tone (VT), into current SEL program impact-assessments and recommends incorporating mind-body practices such as exercise, breathing, mindfulness, and yoga into SEL interventions. This model hypothesizes that the integration of physiological measures and the practices that affect these markers will lead to an increase in SR via a bidirectionally-causative upward spiral. Recommendations for school-based interventions to affect VT are discussed, along with considerations for implementation.