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To create bright and stable fluorescent biolabels for immunoassay detection of mycotoxin deoxynivalenol in food and feed, CdSe/CdS/ZnS core-shell quantum dots (QDs) were encapsulated in silica nanoparticles through a water-in-oil reverse microemulsion process. The optical properties and stability of the obtained silica coated QDs (QD@SiO2), modified with amino, carboxyl and epoxy groups and stabilized with polyethylene glycol fragments, were characterized in order to assess their bioapplicability. The developed co-condensation techniques allowed maintaining 80% of the initial fluorescent properties and yielded stable fluorescent labels that could be easily activated and bioconjugated. Further, the modified QD@SiO2 were efficiently conjugated with antibodies and applied as a novel label in a microtiter plate based immunoassay and a quantitative column-based rapid immunotest for deoxynivalenol detection with IC50 of 473 and 20 ng/ml, respectively.