We developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from nasopharyngeal and oropharyngeal swabs. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler, enabling a fast processing of samples. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and UPLC separation. MS/MS detection of two peptides from SARS-CoV-2 nucleoprotein and their isotope label standards and endogenous control peptides was achieved within 2.5 min, enabling the analysis of more than 500 samples per day.