Cornelian cherry fruit extract rich in anthocyanins and iridoids was encapsulated in the halloysite nanotubes in order to obtain a stable nanoscale system for better delivery and prolonged release of bioactive constituents. The cyclic vacuum technique was used for halloysite nanotubes-cornelian cherry composite preparation and the loading of 8.5 wt% was achieved. Pure cornelian cherry extract exhibited antiproliferative effect on HT-29, MCF7, and MRC-5 cells, pristine halloysite nanotubes affected the growth of MCF7 cells, while halloysite nanotubes-cornelian cherry composites demonstrated proliferative activity in all tested cells. The sustained release of anthocyanins was achieved by this encapsulation strategy. Additional implementation of halloysite nanotubes-cornelian cherry into yogurt prolonged the release of iridoid molecules. Obtained results indicate that halloysite nanoclay is a suitable nanocarrier for cornelian cherry constituents that can be utilized in food and pharmaceutical industries.