In two intensive longitudinal studies we examined the daily dynamics in health behaviors and their associations with two important indicators of young adults’ daily functioning, namely, affect and academic performance. Over a period of 8 months, university students (Study 1: N = 292; Study 2: N = 304) reported sleep, physical activity, snacking, positive and negative affect, and learning goal achievement. A subsample wore an actigraph to provide an additional measurement of sleep and physical activity and participated in a controlled laboratory snacking situation. Multilevel structural equation models showed that better day-to-day sleep quality or more physical activity than usual, but not snacking, were associated with improved daily functioning, namely, affect and learning goal achievement. Importantly, self-report measurements of health behaviors correlated with behavioral measurements. These findings have the potential to inform health promotion programs aimed at supporting young adults in their daily functioning in good physical and mental health.