Primary diagnosis of celiac disease (CD) in rheumatology department is not common in daily clinical practice, due to the fact that diarrhoea is usually the dominant symptom. Extra-intestinal manifestations, such as arthralgia, myalgia, osteomalacia, and osteoporosis are not rare in these patients. We present a case of a 66-year-old man, who came to the outpatient rheumatology clinic, complaining of back and knee pain. Osteopenia was observed in plain radiographs, whereas extensive laboratory testing revealed celiac disease, vitamin D deficiency, and extremely low bone mineral density (BMD) due to osteomalacia. Gluten-free diet (GFD) initiation and administration of vitamin D and calcium supplements resulted in significant symptom and BMD improvement over 6 months. A significant proportion of CD patients might present with arthralgia, arthritis, back pain, myalgia, or bone pain. Importantly, up to 75% of patients might have reduced BMD, due to osteoporosis or osteomalacia, while they also carry a significant risk for fracture. However, the introduction of GFD and calcium/vitamin D supplementation significantly ameliorates symptoms and BMD in most cases. Increased awareness of CD’s musculoskeletal manifestations by rheumatologists is important for early recognition and management of this condition and its complications.