Recess is a critical source of physical, social and emotional health and well-being for children, but generally not prioritized during online learning. A 13-week structured recreation intervention was delivered virtually during recess to students in the fifth and sixth grades (age 10-12 years; N = 71) at one elementary school (Phoenix, AZ, USA). We used embedded mixed method with a prospective pre-/post-design to measure change in student-reported emotion and qualities of engagement in an online setting. Students completed an online pre-/post-survey to measure emotion and motivational responses (enjoyment, competence and relatedness). We used narrative notes to qualitatively assess student engagement during programming. Differences in student-reported emotion were analyzed using paired t-tests. The effect of motivational responses on emotion was analyzed using multiple regression analyses. "In vivo" coding and concept coding were used to analyze qualitative data. We found no statistically significant differences in student-reported emotion; however, student relationships with peers predicted increased positive and decreased negative emotions after the intervention. Seven categories promoted student engagement: challenging, enjoyable, experiential, practical, purposeful, relatable and relevant. School-based health practitioners can offer structured activities virtually during recess, when in-person learning is interrupted and in all-online settings, to promote emotional well-being.