Background: Atrial fibrillation negatively impact physical fitness and health-related quality of life in patients. We recently showed that physiotherapist-led exercise-based cardiac rehabilitation improves physical fitness in patients with permanent atrial fibrillation, however little is known about the effect of detraining after finishing an exercise period. The purpose of the study was to examine the impact of 3 months of detraining on physical fitness, physical activity level and health-related quality of life among patients with permanent atrial fibrillation, after ending a randomized comparison of physiotherapist-led exercise-based cardiac rehabilitation versus physical activity on prescription.Methods: Prospective 3-month follow-up study after a randomized multi-centre study. Of the 87 patients completing the intervention study, 80 (92%) participated in the detraining part (22 women; age 74 ± 5 years), 38 from the physiotherapist-led exercise-based cardiac rehabilitation group and 42 from the physical activity on prescription group. All patients were asked to refrain from organised exercise during the 3-months period of detraining. The primary outcome measure was maximal exercise capacity using an exercise tolerance test. Secondary outcomes measures were muscle function, physical activity level, and health-related quality of life using a muscle endurance tests, Short Form-36, and physical activity assessments (questionnaire and accelerometer), as in the intervention study. We used the Mann-Whitney U-test and X2 test to analyse differences between the groups, and Cohen’s d to determine the effect size. A mixed effect model analysis was used to identify predictors of change in physical fitness.Results: Compared to the physical activity on prescription, physiotherapist-led exercise-based cardiac rehabilitation showed a significantly decreased exercise capacity (−9 ± 11 vs. −2 ± 12 W, P < .0001), reduction in shoulder flexion repetitions (−4 ± 8 vs. 2 ± 7 repetitions, P = .001), and reduced health-related quality of life in the Short Form-36 dimension Role Emotional (−13 ± 39 vs. 6 ± 27 points, P = .006). Conclusion: In elderly patients with permanent atrial fibrillation detraining negatively impacted previously achieved improvements from physiotherapist-led exercise-based cardiac rehabilitation in physical fitness and reduce health-related quality of life. The importance of continued exercise is emphasized and should be part of the strategy. Retrospectively registred in ClinicalTrials.gov Identifier: NCT02493400. First posted July 9, 2015