Halloysite, as an inorganic nanoclay material, maltodextrin, as a carbohydrate polymer, and the composite made of them were tested as encapsulating agents for blackthorn (Prunus spinosa L.) extract rich in phenolic acids and anthocyanins. For the halloysite nanotubes loading cyclic vacuum technique was applied, and maltodextrin encapsulates were prepared by freeze-drying process. Thermogravimetric analysis confirmed that blackthorn extract was encapsulated with halloysite, maltodextrin, and maltodextrin-halloysite composite. The cytotoxic effect of the encapsulates was tested in tumor (MCF7 and HT-29) and non-tumor (MRC-5) cells. The release of four major phenolic compounds: 3-O-caffeoylquinic acid (neochlorogenic acid) and, cyanidin 3-O-glucoside, cyanidin 3-O-rutinoside, and peonidin 3-O-rutinoside was tested. Addition of extract and encapsulates in yoghurt prolonged the release of blackthorn bioactives. These results indicate that blackthorn extract and its halloysite and maltodextrin encapsulates have potential in the production of functional foods, food supplements, and pharmaceuticals.