Pesticide residues in food products cause human health concerns through food contamination, thereby necessitating their rapid and facile detection. Although surface-enhanced Raman scattering (SERS) technique can rapidly and reliably detect pesticide residues, its application in food safety diagnostics is restricted by its high expense, low scalability, and low reproducibility of the necessary sensors. Herein, we present a low-cost, large-scale, and highly reproducible nanofabrication route for SERS nano-sensors, based on the thermophoresis-assisted direct deposition of plasmonic core–shell structured Ag-SiO2 nanoparticles produced in the gas phase, on temperature-controlled inexpensive glass substrates. The high-performance SERS substrates were fabricated at a laboratory production rate of 100 samples/hour, demonstrating the scalability and cost-effectiveness of our aerosol manufacturing strategy. Our highly sensitive SERS substrates rapidly and quantitatively detected pesticide residues in fresh orange, indicating their practical applicability for food safety diagnostics.