Salmonellosis remains one of the leading causes of bacterial gastrointestinal infections in humans and animals. Molecular diagnostics has dramatically reshaped the diagnostic landscape for Salmonella infection; however, it remains time- and resource-intensive. Isothermal DNA amplification, for example loop isothermal amplification (LAMP), performed at a constant temperature, is the basis for the development of rapid diagnostic tests that can be adapted to the point-of-care (PoC) formats and implemented in resource-limited settings or remote from centralized laboratories. The aim of this study was to develop and validate a novel LAMP-based method for detecting Salmonella enterica in human stool samples, wherein amplification results are monitored using a loop primer labeled with a fluorophore and an internal quencher. The proposed method achieves a limit of detection (LoD₉₅) of 250 copies per reaction, with a sensitivity of 86.84% (95% CI: 71.91–95.59%) and specificity of 96.49% (95% CI: 87.89–99.57%) relative to qPCR, and demonstrates increased robustness against DNA amplification inhibitors present in fecal samples. Incorporation of distinct fluorophores into loop primers for FLP-LAMP targeting different genes could potentially enable multiplexing and simultaneous detection of multiple pathogens, thereby expanding the diagnostic utility of isothermal amplification.