This research studied the use of banana purée from three indigenous Thai cultivars (Kluai Hom Thong, Kluai Namwa and Kluai Khai) as probiotic carrying agents in food and application in bio-set-type yoghurt. Kluai Khai purée had promising indication of prebiotic activity on Lactobacillus paracasei Lpc-37 with the highest probiotic activity score. When Lpc-37 cell was incorporated into Kluai Khai purée, its cell counts increased by 0.8 log CFU g−1 and it adhered to purée, as seen by the proliferating cells. Therefore, Kluai Khai purée mixed with Lpc-37 was selected for the production of bio-set-type yoghurt. The results showed that viable cells increased more than 0.8 log CFU g−1 during storage. This study reflected the achievement of using Kluai Khai purée as food matrix for carrying ‘active probiotic cells’ in bio-yoghurt production. This methodologically developed prototype could be an interesting alternative for value adding of indigenous fruits.