Objective: Flourishing is a mental health indicator that helps students function optimally, which may be important for first-year university students. Physical activity (PA) also contributes to optimal functioning, yet the flourishing and PA relationship has received little attention. The bidirectional relationships between flourishing and meeting moderate-to-vigorous PA (MVPA) guidelines were assessed during the first year of university. Methods: First-year university students completed surveys (September [T1], March [T2]). Reciprocal effects were examined in a cross-lagged path model. Results: Over 40% of the sample was not meeting MVPA guidelines at T1 or T2. Controlling for sex, higher T1 flourishing was associated with higher odds of meeting T2 MVPA guidelines. T1 MVPA did not predict T2 flourishing. Conclusions: The findings provide preliminary evidence that flourishing may support meeting MVPA guidelines for first-year students. Given low rates of meeting guidelines, flourishing and PA could be targeted to foster MVPA, supporting a healthy university transition.