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Abstract The residual of pesticides in fruit and vegetables is one of the major food safety concerns for consumers. There is a demand for easy and rapid analytical methods to sense pesticide residues in foods. In this study, a core-shell Au@Ag nanoparticles aggregates (Au@AgNAs) based surface-enhanced Raman scattering (SERS) method was developed to detect trace amount of difenoconazole. Results suggested that by targeting the characteristic peaks at 700 and 808 cm−1, the logarithmic SERS signal intensities and logarithmic difenoconazole concentrations in the range from 5 × 10−7 to 2.5 × 10−5 M showed linear relationship with the coefficient of determination (R 2 ) of 0.990 and 0.985, and limit of detection (LOD) values of 5.01 × 10−8 and 2.8 × 10−8 M, respectively. The Quick Easy Cheap Effective Rugged and Safe (QuEChERS) sample preparation method was used to extract difenoconazole in grapes for SERS measurements. The LOD of difenoconazole in grapes using this developed method was as low as 48 μg/kg, which was significantly lower than the maximum residue limit (MRL) values prescribed by European Union and China. This study demonstrated that the Au@AgNAs-based SERS method can be used as a simple, rapid and sensitive approach for sensing trace contaminants in food. Graphical abstract fx1 Highlights • SERS is an alternative method for rapidly detecting trace contaminants. • Au@Ag nanowire aggregates was used as SERS substrate for detecting pesticide. • The developed SERS method can detect as low as 48 μg/kg difenoconazole in grapes. • The entire analysis can be achieved within 25 min. [ABSTRACT FROM AUTHOR]