Introduction: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are associated with increased risk of bone loss due to chronic inflammation, nutritional deficiencies, and pharmacological treatment.Purpose: The purpose of this study was to evaluate bone mineral density (BMD) and selected bone turnover markers in IBD patients in clinical and endoscopic remission, treated with conventional therapy or anti-TNF-α agents.Methods: This single-center study included 100 participants: 35 with CD, 37 with UC, and 28 age-matched healthy controls. Patients IBD participated in the study received conventional treatment or anti- TNF-α therapy with ADA (adalimumab) or IFX (infliximab). IBD patients were in confirmed remission, without steroid use or comorbidities affecting bone metabolism. BMD was measured using dual-energy X-ray absorptiometry (DXA) at the lumbar spine (L2–L4), the left femoral neck, and whole body. Serum levels of osteocalcin (OC), parathyroid hormone (PTH), sclerostin (SOST), fibroblast growth factor 23 (FGF23), Dickkopf-1 (DKK1), osteoprotegerin (OPG), and osteopontin (OPN) were assessed.Results: The IBD group demonstrated a statistically significant higher OPN value (p < 0.001) compared to the control group. Additionally, the total T-score revealed a significant difference between the groups (p = 0.005), with the control group exhibiting the highest values. No significant differences were found in the levels of other bone density markers studied between the biologically treated group and the conventionally treated group.Conclusions: Our study indicates that patients with IBD are at risk of developing reduced bone mineral density and osteoporosis. While some bone turnover markers appear to normalize during remission, anti-TNF-α treatment does not offer added benefits for bone metabolism compared to conventional therapy.