The study compared bone mineral density (BMD) and markers of bone turnover in 100 patients: 35 with Crohn's disease, 37 with ulcerative colitis, and 28 age-matched healthy controls. Inflammatory bowel disease (IBD) patients were in remission, free of steroids and bone-affecting comorbidities, and received either conventional therapy or anti-TNF-α therapy (adalimumab or infliximab). BMD was measured by the DXA method in the lumbar spine (L2–L4), femoral neck and whole body. The markers evaluated included osteocalcin (OC), parathyroid hormone (PTH), sclerostin (SOST), FGF23, DKK1, osteoprotegerin (OPG) and osteopontin (OPN). The IBD group had statistically significantly higher OPN levels (p < 0.001) and lower total T-scores compared to controls (p = 0.005). No significant differences in markers were found between patients on anti-TNF-α and conventional treatment. The study shows a risk of reduced BMD and osteoporosis in patients with IBD in remission, while anti-TNF-α therapy does not confer additional benefits on bone metabolism compared to conventional treatment.