Proteins are the most common biomacromolecules in biological cells and are used in many applications, such as in food formulations and as therapeutic agents. For these applications, it may be desirable to protect proteins from their environment to preserve their function by packing them into nanocontainers. Therefore, we studied the encapsulation of fluorescent proteins with charged polymers and investigated formation, composition, and dynamics of the resulting nanopackages. We found that the structure and fluorescent properties of the proteins change upon encapsulation, but these changes appeared to be reversible after release of the proteins. Furthermore, we observed that the nanocontainers quickly fall apart upon addition of salt. These findings can be employed to further engineer the nanocontainers and increase their stability for use in practical applications.