In this paper, we implement a Whispering Gallery mode microbubble resonator (MBR) as an optical transducer to detect the photoacoustic (PA) signal generated by plasmonic nanoparticles. We simulate a flow cytometry experiment by letting the nanoparticles run through the MBR during measurements and we estimate PA intensity by a Fourier analysis of the read-out signal. This method exploits the peaks associated with the MBR mechanical eigenmodes, allowing the PA response of the nanoparticles to be decoupled from the noise associated with the particle flow whilst also increasing the signal-to-noise ratio. The photostability curve of a known contrast agent is correctly reconstructed, validating the proposed analysis and proving quantitative PA detection. The experiment was run to demonstrate the feasible implementation of the MBR system in a flow cytometry application (e.g., the detection of venous thrombi or circulating tumor cells), particularly regarding wearable appliances. Indeed, these devices could also benefit from other MBR features, such as the extreme compactness, the direct implementation in a microfluidic circuit, and the absence of impedance-matching material.