Kidney transplant recipients (KTRs) have an elevated fracture risk. While dual-energy X-ray absorptiometry (DXA) is commonly used to assess areal bone mineral density (aBMD), it does not capture all aspects of bone quality. We investigated the long-term effects on bone DXA-derived indices of bone quality in KTRs treated with denosumab and untreated with denosumab. This is a retrospective study, including KTRs treated with denosumab and untreated age and sex-matched KTR controls. DXA-derived parameters, including trabecular bone score (TBS) and 3D-DXA parameters, were measured at the lumbar spine and femur at baseline and after four years. Hierarchical linear models were used to assess the between-group effect of treatment over time, also adjusting for site-specific aBMDs. We enrolled 23 KTRs treated with denosumab and 23 KTR denosumab-untreated KTRs. Significant between-group differences over time in favor of the denosumab group were observed for TBS (0.843, 95%CI 0.439
1.248,p <
0.001), trabecular volumetric BMD at the total hip (Tb.vBMD TH) (13.492, 95%CI 1.707
25.278, p = 0.003), cortical volumetric BMD at the femoral neck (Ct.vBMD FN) (28.766, 95%CI 8.373
49.158, p = 0.008), cortical surface BMD at the total hip (c.sBMD TH) (10.507, 95%CI 4.140
16.873,p = 0.002), cortical surface at the femoral neck (c.sBMD FN) (8.795, 95%CI 2.818
14.771, p = 0.006), and cortical thickness at the total hip (Ct.th.TH) (0.075, 95%CI 0.020
0.130, p = 0.010). After adjusting for BMD, the differences on TBS and Ct.vBMD FN and c.sBMD FN remained significant. Denosumab treatment in KTRs was associated with better outcomes in terms of bone quality and geometry parameters, independent of changes in aBMD.