Background: In the past few decades, the inadequate reprocessing of bronchoscopes has been associated with several serious outbreaks caused by multidrug-resistant microorganisms. In this study we evaluated the improvement in the quality of reprocessing in a Bronchoscopy Unit (BU), after the introduction of a new procedure. Methods: In 2019, observational and clinical audits were conducted in the BU. After the introduction of an improved procedure in 2020, a microbiological surveillance plan was implemented in 2021. Results: In 2019, 13 of 22 bronchoscopes (59%) resulted as non-compliant, 18% as high concern organisms (HCO) and 36.4% as high microbial count (≥100 CFU/all channels) and HCO. The most frequent microorganisms were Staphylococcus aureus (38.5%) and NDM-producing Klebsiella pneumoniae (15.4%). The bronchoscopes were stored inside their transport cases, which in some cases were found to be contaminated by the same strains isolated on the bronchoscopes (Enterobacter gergoviae and Vibrio alginolyticus). In 2021, all 31 bronchoscopes were sampled at least three times and 13/99 (13.1%) resulted as non-compliant, mostly K. pneumoniae (4.04%). Contamination level increases weakly in bronchoscopes in use for more than 14 years (R = 0.32). Conclusions: The adoption of an improved reprocessing procedure decreased the non-compliance of bronchoscopes, increasing the quality of the process and patient safety.