The use, in veterinary practice, of a three-dimensional biopolymer matrix (based on chitosan, agarose, and gelatin and doped with halloysite nanotubes) as a vehicle for mesenchymal stem cells (MSCs) to repair bone defects is reported here. The nanocomposite, combined with allogenic adipose-derived stem cells, was suitable for the repair of bone defects in dogs when paired with standard surgery involving metal Kirshner wires. The absence of inflammatory reactions to biopolymer matrices with allogenic stem cells was revealed in the case of an animal prone to inflammatory and allergic reactions. In addition, positive dynamics in the fusion of chronic bone defects without rejection reactions was observed after using a biopolymer matrix with MSCs.