The high demand for COVID-19 diagnosis overwhelmed reference hospitals. Regional laboratories had to incorporate molecular technology to respond to the emergency. This work described the implementation of molecular diagnostic tools and the detection of SARS-CoV-2, in a regional hospital with no previous experience, from October 2020 to March 2022. The laboratory structure was significantly modified. The staff grew from 3 to 4 clinical microbiologists, and from 7 to 17 laboratory technicians to provide 24/7 coverage. A total of 144,442 samples were processed during the period of study. The highest peaks were reached in July 2021 with 25,285 samples processed, and between December 2021 and January 2022, with 32,245. COVID-19 pandemic has represented not only the challenge, but the opportunity to introduce Nucleic Acid Amplification Techniques (NAAT) in inexperienced laboratories. These secondary settings have shown an extraordinary ability to adapt and cannot be left behind in the progress of diagnostic techniques.