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Background This study aimed to investigate the mediating effect of physical activity enjoyment (PAE) on various physical activity (PA) levels in adult people with cystic fibrosis (pwCF) concerning disease-specific and non-disease-specific factors. Methods A total of 168 adult pwCF (39.3% females; mean age 36.7 ± 11.9 years) completed questionnaires assessing PAE (Physical Activity Enjoyment Scale, PACES) and PA levels (7-day Physical Activity Recall, PAR). Participants’ demographics (age, sex) and clinical characteristics [ppFEV1; percent predicted forced expiratory volume in 1 s, and BMI; body mass index (kg/m2)]) were extracted from medical records. Mediation analysis was used to examine the direct and indirect effects of disease-specific and non-disease-specific factors on PA, considering PAE as a potential mediator. Results Correlation analyses indicated a weak but statistically significant association between ppFEV1 and very vigorous physical activity (VVPA) (r = 0.177; p = 0.021) and PAE (r = 0.221; p = 0.004). PAE was linked to time spent in vigorous physical activity (VPA) (r = 0.202; p = 0.009), VVPA (r = 0.238; p = 0.002), and moderate-to-vigorous physical activity (MVPA) (r = 0.152; p = 0.049). Mediation analysis revealed that PAE fully mediated the association between lung function (ppFEV1) and vigorous PA (VPA), very vigorous PA (VVPA), and moderate-to-vigorous PA (MVPA) but not moderate PA (MPA). PpFEV1 and PAE together accounted for 26–49.3% of the variance in PA, suggesting the presence of other influential factors. No mediation effect was observed between PAE and age and BMI on any of the PA levels Conclusions Our findings underscore the importance of both physiological and psychological factors in shaping PA among adults with CF. Beyond traditional clinical management, strategies that enhance PAE may be crucial for promoting sustained PA engagement. Future research should examine additional psychological and environmental factors influencing PAE and develop comprehensive approaches to support active lifestyles in this population.