Research examined how acute affect dynamics, including stability and context-dependency, contribute to changes in children’s physical activity levels as they transition from late-childhood to early-adolescence. Children (N = 151) (ages 8–12 years at baseline) participated in an ecological momentary assessment and accelerometry study with six semi-annual bursts (7 days each) across three years. A two-stage mixed-effects multiple location-scale model tested random intercept, variance, and slope estimates for positive affect as predictors of moderate-to-vigorous physical activity (MVPA). Multi-year declines in MVPA were greater for children who had greater subject-level variance in positive affect. Children who experienced more positive affect when alone did not experience steeper declines in physical activity. Interventions aiming for long-term modifications in children’s physical activity may focus on buffering the effects of within-day fluctuations in affect or tailoring programs to fit the needs of “acute dynamic process phenotypes.”