Primary synovial chondromatosis is a rare, benign disorder due to metaplastic proliferation of the synovium, leading to the formation of cartilaginous loose bodies. Typically monoarticular and intra-articular, its occurrence in the shoulder is uncommon, and concomitant extra-articular involvement is very rare. Removal of the loose bodies with synovectomy is usually the only standard form of treatment. This is the case of a 23-year-old male patient from Myanmar who presented with a 2-year history of right shoulder pain with progressive limitation of motion. Radiographic and magnetic resonance imaging findings were consistent with chondromatosis, showing multiple loose bodies within the glenohumeral joint, extending to the subcoracoid area and along the extra-articular biceps tendon. Arthroscopic synovectomy, debridement, and removal of loose bodies was performed, with subsequent conversion to open removal of loose bodies. A capsular shift was also performed due to an enlarged inferior pouch and a loosened anterior capsule. This paper presents a rare case of synovial chondromatosis of the shoulder with both intra-articular and extra-articular involvement. The standard of care addresses loose body removal. However, associated problems should be established when dealing with similar problems. In this case, careful preoperative and perioperative evaluation identified other areas affected and dealt with the potential complication of shoulder instability.