Background <p>Understanding barriers to participate in exercise intervention studies is critical for guiding approaches to increase sample representativeness, to mitigate selection bias, and to achieve the required sample size for study purposes. This study compared physical activity levels and exercise-related perceptions, including barriers and facilitators, between liver transplant recipients who were willing <i>versus</i> not-willing to engage in an exercise intervention randomised controlled trial (RCT).</p> Methods <p>A comparative cross-sectional study was conducted using baseline data of the PHOENIX-Liver trial, a RCT evaluating a 6-month home-based exercise intervention followed by a physical activity maintenance program. Two informed consents were obtained from eligible liver transplant recipients (3–5 months post-transplant; &gt;18 years) either willing (<i>n</i> = 64) or not willing (<i>n</i> = 46) to participate. Clinical and sociodemographic characteristics were collected from electronic medical records and questionnaires. Physical activity was assessed objectively (accelerometry) and subjectively (Physical Activity Vital Sign Questionnaire). Exercise-related barriers and facilitators were measured using the Motivators and Barriers Questionnaire.</p> Results <p>42% of 110 eligible individuals declined participation, most often due to time constraints (40%), transportation challenges (25%), and lack of motivation (15%). Non-participants were significantly more likely to have lower education (<i>p</i> = 0.009), lower income (<i>p</i> = 0.004), and live farther from the study site (<i>p</i> = 0.004). Self-reported physical activity levels did not differ between groups, but accelerometry showed that non-participants spend less time in moderate-to-vigorous physical activity (<i>p</i> = 0.05) and took fewer daily steps (<i>p</i> = 0.01). Multivariate logistic regression showed trends for greater distance from centre (<i>p</i> = 0.056), lower education (<i>p</i> = 0.082), and lack of motivation/time (<i>p</i> = 0.071) with unwillingness to participate. High income was independently associated with meeting WHO physical activity guidelines (<i>p</i> = 0.049).</p> Conclusion <p>A substantial proportion of eligible individuals declined participation. Some sociodemographic and behavioural barriers point to potential selection bias. Addressing these through tailored study designs could enhance engagement, improve representativeness and support the recruitment of representative patient populations in future exercise interventions.</p> Clinical trial registration number <p>NCT06302205 (trial registration date: 06/12/2023).</p>