Core-shell fibers are emerging as interesting microstructures for the controlled release of drugs, proteins, and complex biological molecules, enabling the fine control of microreservoirs of encapsulated active agents, of the release kinetics, and of the localized delivery. Here we load luminescent molecules and enhanced green fluorescent proteins into the core of fibers realized by coaxial electrospinning. Photoluminescence spectroscopy evidences unaltered molecular emission following encapsulation and release. Moreover, the release kinetics is microscopically investigated by confocal analysis at individual-fiber scale, unveiling different characteristic time scales for diffusional translocation at the core and at the shell. These results are interpreted by a two stage desorption model for the coaxial microstructure, and they are relevant in the design and development of efficient fibrous systems for the delivery of functional biomolecules.