Objective: Habits, defined as well-learned associations between cues and behaviours, are essential for health-related behaviours, including physical activity (PA). Despite the sensitivity of habits to context changes, little remains known about the influence of a context change on the interplay between PA habits and behaviours. We investigated the evolution of PA habits amidst the spring COVID-19 lockdown, a major context change. Moreover, we examined the association of PA behaviours and autonomous motivation with this evolution. Design: Three-wave observational longitudinal design. Methods: PA habits, behaviours, and autonomous motivation were collected through online surveys in 283 French and Swiss participants. Variables were self-reported with reference to three time-points: before-, mid-, and end-lockdown. Results: Mixed effect modelling revealed a decrease in PA habits from before- to mid-lockdown, especially among individuals with strong before-lockdown habits. Path analysis showed that before-lockdown PA habits were not associated with mid-lockdown PA behaviours (β = -.02, p = .837), while mid-lockdown PA habits were positively related to end-lockdown PA behaviours (β = .23, p = .021). Autonomous motivation was directly associated with PA habits (ps < .001) and withto before- and mid-lockdown PA behaviours (ps < .001) (but not with end-lockdown PA behaviours) and did not moderate the relations between PA behaviours and habits (ps > .072). Conclusion: PA habits were altered, and their influence on PA behaviours was impeded during the COVID-19 lockdown. Engagement in PA behaviours and autonomous motivation helped in counteracting PA habits disruption.