Rheumatoid arthritis (RA) is associated with systemic bone loss and thus an established risk factor for osteoporosis. Janus kinase inhibitors (JAKi) have shown osteo-protective effects. However, clinical data on the effects of baricitinib on bone mineral density (BMD) remain limited. Therefore, we investigated the effects of a 1-year treatment with baricitinib on BMD in RA patients. Patients with active RA beginning treatment with baricitinib were included. BMD was measured at the lumbar spine and femoral neck using Dual-Energy X-Ray Absorptiometry (DXA). Disease activity was assessed using DAS28-CRP and cDAI. The primary endpoint was the change in BMD after 12 months. Secondary endpoints evaluated changes in disease activity, prednisolone dose and alkaline phosphatase (AP) levels and its relation to BMD. A total of 46 RA patients were recruited, of whom 26 completed the study. Overall, BMD remained stable. Non-responders to baricitinib (based on DAS28-CRP) showed a significant decline in spine BMD (- 2.12%, p = 0.039), while responders showed stable BMD. The between-group difference in spine BMD (p = 0.008) and T-score (p = 0.012) was significant. Demographic and clinical characteristics did not differ significantly between groups. Disease activity (DAS28-CRP: p = 0.003; cDAI: p = 0.007), prednisolone dose (p = 0.006), and AP levels (p = 0.03) all improved significantly. Under baricitinib, BMD loss appeared stabilized in RA patients. Non-responders to baricitinib experienced a significant loss of BMD with a significant difference to responders raising the question if seen effects are achieved by controlling disease activity or if there is an additional explicit JAKi effect on bone metabolism. Trial registration number: DRKS00020780, date: 13.3.2020.