Fluorescent semiconductor nanocrystals or quantum dots (QDs) are characterized by unique optical properties, including a high photostability, wide absorption spectrum, and narrow, symmetric fluorescence spectrum. This makes them attractive fluorescent nanolabels for the optical encoding of microcarriers intended for targeted drug delivery, diagnosis, and imaging of transport processes on the body, cellular, and subcellular levels. Incorporation of QDs into carriers in the form of polyelectrolyte microcapsules through layer-by-layer adsorption of oppositely charged polyelectrolyte polymers yields microcapsules with a bright fluorescence signal and adaptable size, structure, and surface characteristics without using organic solvents. The easily modifiable surface of the microcapsules allows for its subsequent functionalization with capture molecules, such as antibodies, which ensures specific and selective interaction with cells, including tumor cells, with the use of the bioconjugation technique developed here. We obtained stable water-soluble nanolabels based on QDs whose surface was modified with polyethylene glycol (PEG) derivatives and determined their colloidal and optical characteristics. The obtained nanocrystals were used to encode polyelectrolyte microcapsules optically. The microcapsule surface was modified with humanized monoclonal antibodies (Abs) recognizing a cancer marker, epidermal growth factor receptor (EGFR). The possibility of effective, specific, and selective delivery of the microcapsules to tumor cells expressing EGFR has been demonstrated. The results show that the QD-encoded polyelectrolyte microcapsules functionalized with monoclonal Abs against EGFR can be used for targeted imaging and diagnosis.