Photoacoustic flow cytometry (PAFC) is an emerging technology that has generated significant interest in several research fields, particularly in bacteremia. The application of functionalised nanoparticles like gold and iron oxide-gold complex (Fe3O4-Au) has been realised to enhance the photoacoustic (PA) detection of bacteria cells under PAFC systems. Inclusively, the bacteria cell concentrations are statistically quantified through the number of time-signal detection counts. This study uses a similar technique by using gold (Au) and magnetite-gold complex (Fe3O4-Au) nanoparticles in the PAFC system to improve the detection of Salmonella LT2 (SLT2) cells under 532 nm laser irradiation, resulting in over a 200 % increase. However, this study’s contribution comes from the post-processing and analysis of PA time signals after exposing various concentrations of SLT2 cells. Upon fast Fourier transform (FFT) analysis of time signals, a distinct peak frequency at 2.75 MHz was significantly attributed to SLT2 as its likely acoustic frequency fingerprint, even at its lowest concentrations (10 CFU/ml). Furthermore, an electromagnetic wave simulation (optical scattering and heat transfer in fluids) was employed to distinguish the PA and Photothermal contributions of the nanoparticles in the system. The resulting data consolidates the continuous wave transform (CWT) of the time signal, where 22.5 – 30 µs was strongly affiliated with PA, and 32–40 µs was that of the photo-thermal-acoustic effect—indicating that both signals can be used to detect and potentially confirm the eradication of SLT2 cells. Overall, magnetised Fe3O4-Au nanoparticles yielded more efficiency through its reproducible PA time signals with 0.84 standard deviations, and its 2.75 MHz frequency peak area matches most accurately with the SLT2 cell concentration by 97.3 %.