We have studied the optomechanical performance of optical microcantilevers fabricated with integrated waveguides for the on-chip and real-time detection of biorecognition events. The nanomechanical photonic device consists of an optical microcantilever with on-chip integrated waveguides for both coupling the light and detecting the microcantilever response. The photonic device was designed to reach a high sensitivity with a low deflection noise density (DND) of only 0.13fm/√ Hz. The BioMEMS transducer is embedded into a proper designed PMMA/PDMS microfluidic header and connected to a flow delivery system to study the response of the fully-integrated device under physiological conditions. As a proof of concept, we have studied the photonic microcantilever bending during consecutive formation of ultrathin polyelectrolyte multilayer films (electrostatic binding) and during biofunctionalization and biorecognition of the human growth hormone. The read-out platform was developed based on a single laser-single acquisition channel. To avoid the effect of external factors such as device positioning or temperature fluctuations, an automatized light coupling system keeps on tracking the laser beam focused into an input waveguide, increasing the required reproducibility needed for BioMEMS devices and paving the way for a potential portable multichannel sensor platform.