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Well-being and cognition are linked in adulthood, but how the two domains interact during development is currently unclear. Using a complex systems approach, we preregistered and modeled the relationship between well-being and cognition in a prospective cohort of 1,136 children between the ages of 6 to 7 years and 15 years. We found bidirectional interactions between well-being and cognition that unfold dynamically over time. Higher externalizing symptoms in childhood predicted fewer gains in planning over time (standardized estimate [β] = −0.14, p = .019), whereas higher childhood vocabulary predicted smaller increases in loneliness over time (β = −0.34, p ≤ .001). These interactions were characterized by modifiable risk and resilience factors: Relationships to parents, friendship quality, socioeconomic status, and puberty onset were all linked to both cognitive and well-being outcomes. Thus, cognition and well-being are inextricably intertwined during development and may be malleable to social and biological factors.