Salmonella is a bacterial pathogen which is one of the leading causes of severe illnesses in humans. The current study involved the design and development of two methods, respectively using iron oxide nanoparticle (IONP) and iron core gold nanoparticle (ICGNP), conjugated with the Salmonella antibody and the fluorophore, 4-Methylumbelliferyl Caprylate (4-MUCAP), used as an indicator, for its selective and sensitive detection in contaminated food products. Twenty double-blind beverage samples, spiked with Salmonella enteritidis, Staphylococcus aureus, and Escherichia coli, were prepared in sterile Eppendorf® tubes at room temperature. The gold layer and spikes of ICGNPs increased the surface areas. The ratio of the surface area is 0.76 (IONPs/ICGNPs). The comparative sensitivity and specificity of the IONP-based and the ICGNP-based methods to detect Salmonella were determined. The ICGNP method shows the limit of detection is 32 Salmonella per mL. The ICGNPs had an 83.3% sensitivity and a 92.9% specificity value for the presence and detection of Salmonella. The IONP method resulted in a limit of detection of 150 Salmonella per mL, and a 66.7% sensitivity and 83.3% specificity for the presence and detection of Salmonella. The higher surface area of ICGNPs increases the efficiency of detection. The monitoring of Salmonella can thus be achieved by a rapid magnetic fluorescent assay using a smartphone for image capture and analyze, providing quantitative results. The findings from the present study would help to detect Salmonella rapidly in water. It can improve the microbial quality of water and food safety due to the presence of Salmonella in the water environment.