Exercise rehabilitation programmes are important for long-term health and wellbeing among people with cardiac and pulmonary diseases. Despite this, many people struggle to maintain their physical activity once rehabilitation ends. This repeated measures study tracked changes in physical activity behaviour and motivation during and after completing a community-based exercise rehabilitation programme. Cardiac and pulmonary exercise rehabilitation patients (N = 31) completed six once-monthly measures of physical activity (MET·min), self-determined motivation, intention, and habit strength for rehabilitation exercise (within rehabilitation sessions) and lifestyle physical activity (outside of rehabilitation sessions). Linear regression and random effects models with estimated marginal means were used to test for associations between physical activity motivation and behaviour and change during and post-rehabilitation. Overall physical activity decreased after rehabilitation (823 MET·min) despite patients becoming more self-determined for lifestyle physical activity during rehabilitation. More self-determined motivation, stronger intentions, and stronger habits were associated with more lifestyle physical activity behaviour. However, none of these motivation variables were significantly associated with rehabilitation exercise behaviour. Among community-based cardiac and pulmonary rehabilitation patients, physical activity levels decreased following exercise rehabilitation programmes. The findings revealed clear distinctions in the motivation of rehabilitation exercise compared to lifestyle physical activity. Exercise rehabilitation programmes might improve the longevity of outcomes by integrating approaches to enhance lifestyle physical activity beyond the clinic.