Abstract: Background: Two automatable in-house protocols for high-troughput RNA extraction from nasopharyngeal swabs for SARS-CoV-2 detection have been evaluated.Methods: One hundred forty one SARS-CoV-2 positive samples were collected during a period of 10-days. In-house protocols were based on extraction with magnetic beads and designed to be used with either the Opentrons OT-2 (OT-2_in-house) liquid handling robot or the MagMAX^TMExpress-96 system (MM_in-house). Both protocols were tested in parallel with a commercial kit that uses the MagMAX^TMsystem (MM_kit). Nucleic acid extraction efficiencies were calculated from a SARS-CoV-2 DNA positive control.Results: No significant differences were found between both in-house protocols and the commercial kit in their performance to detect positive samples. The MM_kitwas the most efficient although the MM_in-housepresented, in average, lower Cts than the other two. In-house protocols allowed to save between 350€ and 400€ for every 96 extracted samples compared to the commercial kit.Conclusion: The protocols described harness the use of easily available reagents and an open-source liquid handling system and are suitable for SARS-CoV-2 detection in high throughput facilities.