Abstract The design of a novel and reliable plasmonic platform for detecting multiple chemical contaminants in the complex matrix is an exciting topic in the food industry. Herein, a high-performance surface-enhanced Raman scattering (SERS) two-dimensional (2D) nanodot array was designed through liquid-liquid interfacial self-assembly of the core-shell nanoparticles (Au@Ag NPs) and exploited for assessment of dual-fungicides in pear, apple, and orange juices. The 2D Au@Ag nanodot array delivered good uniformity and reproducibility with the substrate-to-substrate relative standard deviation values of 10.51%. This substrate could be used for detecting thiram and thiabendazole in aqueous solutions with the limit of detection of 0.0011 and 0.051 ppm, respectively. Furthermore, satisfactory recoveries ranging from 76–134% for the juices were obtained, demonstrating that the high-throughput 2D Au@Ag nanodot arrays are promising for their applications as sensitive SERS platforms for monitoring chemical contaminants in food products, especially in the beverage industry.