Manual wheelchair use may determine shoulder joint overload and rotator cuff injury. Chronic shoulder pathologies can also influence the propulsion ability of wheelchair athletes with spinal cord injury (SCI) during sport activities. However, the relationship between shoulder pathology and wheelchair performances has never been explored. Therefore, the study aimed to investigate the correlation between shoulder pathologic findings with clinical tests and ultrasonography evaluation and the results of wheelchair performance tests. Nineteen quadriplegic wheelchair rugby players were evaluated to investigate the association between clinical and ultrasound shoulder pathologic findings and their correlation with the performance of field-based selected wheelchair skills tests (WSTs). The outcome measures were the International Wheelchair Rugby Classification Score, dominant and non-dominant Physical Examination Shoulder Score, and dominant and non-dominant Ultrasound Shoulder Pathology Rating Scale (USPRS). The WST was measured at the beginning and at one-year follow-up. A statistically significant correlation was found between the time since SCI and dominant USPRS (p < 0.005). The non-dominant USPRS was strongly related to WST at the beginning (p < 0.005) and the end of the study (p < 0.05). Data suggest that the severity of the non-dominant shoulder pathology detected on the ultrasound is related to lower performance on the WST. Chronic manual wheelchair use could be responsible for dominant SCI shoulder joint and rotator cuff muscle damage, while non-dominant USPRS could be related to performance on the WST.