The devastating outbreak of COVID-19 has posed serious challenges for the diagnostics laboratories, often facing global shortage of reagents and equipment. This study aimed at evaluating an additional RNA extraction method respect to those already recommended by WHO and CDC. A new protocol for RNA extraction from nasopharyngeal swab was set up, adapting the Qiagen RNeasy 96 plate for cell lines, and validated on a set of 96 clinical samples analyzed in parallel by a recommended method. The internal control and target genes analysis showed a good agreement between the two extraction methods, indicating that the two approaches can be considered equivalent for the SARS-CoV-2 diagnostics. The addition of this extraction method can help in increasing the throughput for SARS-CoV-2 molecular test, even in a low automation setting. The data set published in Zenodo is the full data analysed in the paper.