Systemic sclerosis (SSc) is an autoimmune disorder with a high mortality rate from pulmonary manifestations, such as interstitial lung disease and pulmonary hypertension, seen at autopsy in 90% and 75% of patients, respectively. Bronchiolitis obliterans with organizing pneumonia (BOOP) has numerous causes, but it has only been reported in three patients with SSc. We present three cases of biopsy-proven BOOP in patients with scleroderma spectrum disease, including diffuse cutaneous SSc, mixed connective tissue disease with SSc features, and limited cutaneous SSc that later evolved to dermatomyositis/SSc overlap. BOOP and SSc alveolitis have similar findings on spirometry, radiographs, and BAL; the definitive diagnosis of BOOP was therefore made by open lung biopsy. Cyclophosphamide is the current treatment of alveolitis associated with SSc, whereas high-dose prednisone is used to treat BOOP. As a result of this difference, we emphasize the importance of a thorough investigation of pulmonary disease in SSc patients to exclude BOOP and treat appropriately.