We examined whether specific behavioral encouragements could have short-term effects on students’ cognitive performance and affective well-being in daily life. Cross-sectional research suggests positive relationships between physical activity and executive functioning, though findings on short-term effects of physical activity on children's executive functions remain inconsistent. Moderate to vigorous physical activity, however, has been linked to short-term improvements in affective well-being. Breathing exercises were shown to reduce anxiety and increase feelings of relaxation and may therefore provide another easy to implement strategy to improve affective well-being. We conducted a micro-randomized trial with fifth and sixth-grade students (N = 245) in which experimental conditions were randomly assigned to measurement points (at the class-level). Students provided responses to ecological momentary assessments (EMAs) over 20 school days, with four measurements per day (morning n = 3358, school n = 3176, afternoon n = 2554, evening n = 2881). EMAs covered subjective experiences (including sleep-quality, affect, worries) and a working memory task, while physical activity was passively monitored. Experimental conditions included (1) physical activity breaks on 10 school days, (2) breathing exercises on 10 evenings, and (3) 10 control occasions in school and evening sessions with no intervention. Contrary to expectations, physical activity breaks had no significant effects on working memory accuracy, but reduced negative affect. Breathing exercises improved relaxation, especially on days where students reported above-average levels of worries. We will further highlight analyses on individual differences in these relationships and discuss implications of our findings for the development of personalized and adaptive interventions.