Background: The coronavirus disease 2019 (COVID-19) pandemic outbreak has posed new problems in the context of patients suffering from other diseases. In particular, musculoskeletal sequelae related to the state of debilitation associated with COVID-19 are important to consider in elderly patients undergoing surgery after lower limbs fracture, especially in the post-operative period. The objective of this study was to evaluate whether COVID-19 influenced biochemical parameter, recovery and mortality of surgically treated patients suffering from lower extremity fractures. Methods: Laboratory and clinical data of 30 patients were extrapolated and analyzed in the pre-operative and post-operative periods. Among these patients, 13 had COVID-19 infection (COVID-19 +), whereas 17 had no signs of COVID-19 infections (COVID-19 −). Long-term clinical and functional outcomes were also analyzed. Results: Lower calcium, slightly higher values of CRP and much higher values of CPK and AST were observed pre-operatively in COVID-19 + patients, who also showed higher prevalence of long-term sequelae than COVID-19 − patients. Conclusions: COVID-19 affects long-term outcome of elderly patients with lower limb fractures in a multifactorial way. First, the virus directly damages the muscle tissue. Secondly, the lung function impairment worsens the overall performance, making rehabilitation more challenging.