An innovative bimetallic gold-silver core–shell nanoflowers (Au@Ag-CSNFs) SERS substrate has been synthesized by a facile electrochemical reduction process on an indium tin oxide (ITO) glass with a total fabrication time of 3 min. The proposed Au@Ag-CSNFs SERS substrate has been distributed evenly with numerous interstices and cavities between each branch, suggesting potential target trap sites and “hot spots”. The Au@Ag-CSNFs administered good reproducibility of SERS signals collected from 140 random spots with a relative standard deviation and an enhancement factor of 13.62 % and 0.9 × 107, respectively. The substrate was further extended for the label-free SERS sensing of thiram residues with an ultra-low detection limit of 7.088 × 10-8 mol/L. The designed probe was further subjected to thiram determination in real milk and juice samples with satisfactory recoveries (91.76–109.40 %). The rapidly synthesized Au@Ag-CSNFs substrate can be extended for SERS sensing in a variety of hazards in food settings.