A nanocomposite based on nanofibrillar cellulose (NFC) coated with gold-silver (core-shell) nanoparticles (Au@Ag NPs) was developed as a novel surface-enhanced Raman spectroscopy (SERS) substrate. SERS performance of NFC/Au@Ag NP nanocomposite was tested by 4-mercaptobenzoic acid. The cellulose nanofibril network was a suitable platform that allowed Au@Ag NPs to be evenly distributed and stabilized over the substrate, providing more SERS hotspots for the measurement. Two pesticides, thiram and paraquat, were successfully detected either individually or as a mixture in lettuce by SERS coupled with the nanocomposite. Strong Raman scattering signals for both thiram and paraquat were obtained within a Raman shift range of 400-2000 cm and a Raman intensity ~ 8 times higher than those acquired by NFC/Au NP nanocomposite. Characteristic peaks were clearly observable in all SERS spectra even at a low concentration of 10 μg/L of pesticides. Limit of detection values of 71 and 46 μg/L were obtained for thiram and paraquat, respectively. Satisfactory SERS performance, reproducibility, and sensitivity of NFC/Au@Ag NP nanocomposite validate its applicability for real-world analysis to monitor pesticides and other contaminants in complex food matrices within a short acquisition time. Graphical abstract.