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Food poisoning and infectious diseases caused by <i>Salmonella typhimurium</i> (<i>S. typhimurium</i>) are serious public health concerns for human health and food safety. The diversity and complexity of food matrices pose great challenges for rapid and ultra-sensitive detection of <i>S. typhimurium</i> in food samples. A method capable of identification, detection, and quantification of <i>S. typhimurium</i> is essential for addressing these issues. In this study, aptamer-coated magnetic beads (Apt-MBs) are employed as capture bio-probes to specifically and selectively concentrate <i>S. typhimurium</i> in food samples. A self-priming chip-based digital PCR was then presented as another biosensor for on-site detection and quantification of <i>S. typhimurium</i> cells. The chip we developed was robust and did not require any external power for sample loading. The combination of Apt-MBs with an on-chip digital detection realized the integration into lab-on-a-chip-based biosensors for on-site monitoring of foodborne pathogens. It was possible to capture and detect <i>S. typhimurium</i> cells as low as 90 CFU/reaction with a capture efficiency of 94.5%. Additionally, the whole process only took about 2 h. This unique platform could also be used to monitor other target bacteria with high specificity and sensitivity by utilizing different aptamers. Furthermore, the platform has potential applications in point-of-care testing in the future.