The aim of the study is to investigate the association between adherence to spinal cord injury-specific physical activity guidelines in manual wheelchair users with spinal cord injury and shoulder pain prevalence. This is a cross-sectional analysis of the SwiSCI Community Survey 2022 data, assessing aerobic activity and muscle strength training adherence in manual wheelchair users with spinal cord injury and shoulder pain prevalence. Logistic regression analysis was used to identify the association between meeting the physical activity guidelines and shoulder pain. Low adherence to aerobic activity and strength training guidelines are observed, with 46% and 64% of the study sample not meeting the respective guidelines. The low adherence to physical activity guidelines contrasts with the general Swiss population from which around 75% is physically active for more than 2.5 hrs a week. Manual wheelchair users present a high prevalence of shoulder pain (40%) and nonadherence to aerobic guidelines in the study sample correlates with 1.55-1.97 higher odds of having shoulder pain. Aerobic activity adherence is associated with lower shoulder pain prevalence, emphasizing its potential for injury prevention. Overall, the presented findings necessitate further longitudinal studies and interventions for a comprehensive understanding and effective management of shoulder pain in manual wheelchair users with spinal cord injury.