Partial substitution of cow milk with ewe or goat milk in pasta filata cheese production had an effect on physicochemical, microbiological, and sensorial characteristics of the final products. The different compositions of raw milk contributed to the peculiar sensorial attributes of the innovative produced cheeses, also influenced by the native microbiota of the different milks. All innovative and traditional Caciocavallo cheeses showed a satisfactory nutritional, sensorial, and microbiological quality. Moreover, considering the peculiar nutritional properties of goat milk, the realized mixed goat Caciocavallo cheeses could lead to good success among consumers interested in healthy foods. The development of appropriate technologies for the production of innovative cheeses using a mixture of cow and ewe or goat milk, with proper characteristics and satisfactory acceptance by consumers, could be an interesting and feasible opportunity for the dairy industry, allowing its expansion in the market. In addition, considering the almost total absence of scientific papers on these types of pasta filata cheeses, the obtained results could give more insight into the characterization of these products.