The use of nanocomposites based on biopolymers and nanoparticles for controlled drug release is an attractive notion. We used halloysite nanotubes that were promising candidates for the loading and release of active molecules due to their hollow cavity. Gel beads based on chitosan with uniformly dispersed halloysite nanotubes were obtained by a dropping method. Alginate was used to generate a coating layer over the hybrid gel beads. This proposed procedure succeeded in controlling the morphology at the mesoscale and it had a relevant effect on the release profile of the model drug from the nanotube cavity.