The present research introduces the concept of developing a novel nanohybrid system based on fluorescent quantum dots coupled to polymer–protein bioconjugates for the detection of potential biological hazards. The organic–inorganic hybrids were constructed by the chemical conjugation of carboxylic functionalized poly(vinyl alcohol) with the designed synthetic recombinant protein specific to bovine herpesvirus (rHBoV5), followed by coupling to II–VI semiconductor quantum dots (QDs). These nanostructures were characterized by UV-visible spectroscopy, Fourier transform infrared (FTIR) spectroscopy, photoluminescence (PL) spectroscopy, and transmission electron microscopy (TEM). The results clearly showed that the polymer–protein bioconjugates (PVA–COOH/rHBoV5) were synthesized via the proposed zero-length linker route. Moreover, these bioconjugates proved to be successful capping agents for producing CdS and CdSe quantum dots using aqueous colloidal chemistry. The TEM images associated with the optical absorption results indicated the formation of nanocrystals with estimated diameters in the range of 4.0–5.0 nm. The “blue-shift”, in the visible absorption spectra, and the PL values present strong evidence that the CdS and CdSe QDs behaved as fluorophores in the quantum-size confinement regime. Finally, the hybrid system was validated by immunochemical assay of bovine herpesvirus utilized as the model for detecting biological hazards. This research opens a window of opportunity of using a new class of hybrid nanomaterials for the rapid detection of potentially threatening biological species.