Permeability is the key property of nanocapsules because it dictates the release rate of encapsulated payloads. Herein, we engineer the crystallinity of polymers confined in the shell of nanocapsules. Nanocapsules with crystalline shells are formed from polyurea and polyphosphoester. The thermal properties, such as crystallization temperature and degree of crystallinity, are different from the bulk. The degree of crystallinity is used to control the shell permeability and, therefore, the release of encapsulated payloads, such as fluorescent dyes, typically used as model components for biomedical applications.