An optimum SERS performance is mainly dependent on the development of innovative substrates that show high spectral reproducibility and stability. The current study involves the synthesis of core–shell nanorods (Au@AgNRs) functionalized with mercaptoacetic acid (MAA) to increase the stability and sensitivity of the substrate for cost-effective and sensitive assessment of paraquat (PQ) residues in fruit samples. The morphological analysis of the substrate using TEM and STEM-EDS images indicated the uniformity in size and structure of the prepared nanoparticles. Further the modified substrate, MAA/Au@AgNRs showed excellent stability and sensitivity in comparison with its unmodified counterpart. For the evaluation of PQ residues in pear and apple fruit samples the modified substrate exhibited R 2 values of 0.9954 and 0.9914 with a low limit of detections of 0.012 and 0.024 ppm, and good percent recoveries of 80–110 % and 81–104 %, respectively. Thus, the study proved the effectiveness of the proposed MAA/Au@AgNRs substrate for assessing residues of herbicide in complex foods.