Bovine mastitis (BM) is a prominent inflammatory disease affecting the dairy industry worldwide, originated by pathogenic agent invasion onto the mammary gland. The early detection of new BM cases is of high importance for infection control within the herd. During inflammation, various biomarkers are released into the blood circulation, which are consequently found in milk. Herein, the lysosomal activity of N-acetyl-β-d-glucosaminidase (NAGase), a predominant BM indicator, was utilized for highly sensitive clinical state differentiation. The latter is achieved by the precise addition of tetraethyl orthosilicate-coated zinc oxide nanostructures (quantum dots or nanoparticles, individually) onto a conventional assay. Enhanced fluorescence due to the nanomaterial accumulative near-field effect is achieved within real milk samples, contaminated with Streptococcus dysgalactiae, favoring quantum dots over nanoparticles (>7-fold and 3-fold, respectively), thus revealing significant differentiation between various somatic cell counts. The main advantage of the presented sensing concept, besides its clinically relevant concentrations, is the early bio-diagnostic detection of mastitis (subclinical BM) by using a simple and cost-effective experimental setup. Moreover, the assay can be adapted for BM recovery prognosis evaluation, and thus impact on udder health status, producing an alternative means for conventional diagnosis practices.