Background: During the first two years after lung transplantation (LTx), the incidence of fragility fractures (FX) is estimated to be 15–50% and it is lower in patients with cystic fibrosis (CF) as compared with other end-stage lung diseases (nCF). The aim of our study is to compare the skeletal outcomes, after the first 2 years post-LTx, in long-term survivors with CF and nCF. Materials and Methods: We evaluated the FX rate, the changes in bone mineral density (BMD) and trabecular bone score (TBS) in 68 patients (38 CF and 30 nCF) who underwent LTx in our center and with a follow-up after LTx longer than 5 years (7.3 ± 2.0 years). Results: After the second year post-LTx: (i) the FX rate was lower than during the first two years post-LTx (4.4 vs. 20.6%, p = 0.004), with no difference between CF and nCF patients (5.3 vs. 3.3%, p = 0.589); (ii) BMD at lumbar spine, femoral neck and total hip remained stable (−1.6 ± 1.0 vs. −1.4 ± 1.1, p = 0.431, −1.8 ± 0.9 vs. −1.9 ± 0.9, p = 0.683, −1.5 ± 0.9 vs. −1.4 ± 0.9, p = 0.678, respectively) as well as TBS (1.200 ± 0.124 vs. 1.199 ± 0.205, p = 0.166). Conclusions: After the second year post-LTx, the skeletal complications become less frequent and have similar incidence in patients with CF and nCF.