Physical activity (PA) is key to improve the prognosis of patients with chronic coronary syndrome (CCS). This study investigated changes in movement behaviors (MB), obesity markers, cardiorespiratory fitness (VO2peak), cardiometabolic risk (CMR), and brain-derived neurotrophic factor (BDNF) and whether changes in MB are associated with VO2peak, CMR, and BDNF from baseline to 9 months after a 12-week exercise intervention. In total, 35 CCS patients (M = 69.5 ± 6.4 years; 82.9% men) underwent a group-based intervention; including two 1-h exercise sessions per week Data was collected on anthropometrics, blood samples, cardiopulmonary exercise testing, and 7-day accelerometry at baseline, 3-month, and 12-month follow-up. Absolute changes were examined using paired t-tests. Mixed-effects linear regression models were applied to investigate associations of MB with VO2peak, CMR, and BDNF over time. Intra-class correlations were calculated to estimate within-person variability. From baseline to 3-month follow-up, light PA (23.7 min/d ± 10.9) increased and body mass index (-0.3 kg/m2 ± 1.2), glucose (-0.8 mmol/L ± 0.3), and diastolic blood pressure (-2.7 mmHg ± 1.3) decreased. From baseline to 12-month follow-up, there were no changes in any marker. Regression models revealed no associations between any measure of habitual movement behaviors and VO2peak, CMR, and BDNF over time. To conclude, short-term but no long-term changes in MB and cardiovascular health markers were observed among CCS patients after a 12-week exercise intervention. Modeling the associations between MB and VO2peak, CMR, and BDNF over time revealed considerable within-person variability in the data, which should be considered in future research. TRIAL REGISTRATION: NCT06178263, Retrospectively registered (20/12/2023).