Apple (Malus domestica) and mango (Mangifera indica L.) pulps were used as a prebiotic in the fortification of flavoured probiotic stirred yoghurt. Flavoured probiotic stirred yoghurt was made from cow's milk supplemented with apple and mango pulps at levels of 5.0, 10.0 and 15%. Resultant stirred yoghurt of all treatments was stored at 5^˚C for 15 days to study the physico-chemical, microbiological, organoleptic and colour properties (L^*, a^*, b^*) of yoghurt samples during storage period. Addition of apple and mango pulps to cow's milk increased acidity, total solids, but decreased total protein, total fat content and pH values of resultant flavoured probiotic stirred yoghurt. Also apple and mango pulps addition improved starter activity, increased total bacterial, bifidobacterial and lactobacilli bacterial counts of resultant flavoured probiotic stirred yoghurt. Colour characteristics (L^*, a^*, b^*) are varied according to the kinds of fruit pulp used in yoghurt, which caused changes in colour of the yoghurt samples. These observations were associated with the level of mango and apple pulp addition. As a result of the organoleptic evaluations, 10% apple pulp yoghurt sample had the highest overall acceptability. Yoghurt with 10% fruit pulp, especially apple pulp could be recommended for large scale production of fruit probiotic yoghurt.