Agro-industrial wastes have emerged as a significant source of bioactive compounds. Therefore, this study was conducted to evaluate the feasibility of using nano-powders of some fruit wastes, namely; apricot (Prunus sp.) and peach (Prunus persica L. Batsch) kernels, watermelon (Citrullus lanatus) rind and banana (Musa spp.) peel as functional ingredients (0.5%) in stirred yoghurt, as well as their effect on the antioxidant activity, quality characteristics, viability of yoghurt starter culture and sensory attributes. Results revealed that the fortification process significantly (P < 0.05) elevated the total solids, fat, protein and ash contents, especially with apricot and peach kernels (AK and PK), which distinctly increased fat by average values of 3.46 and 3.40%, and protein by 3.70 and 3.68% during storage compared to control (3.12 and 3.57%), respectively. The addition of watermelon rind (WMR) increased the titratable acidity (0.97%) and viscosity (463.59 cP) with a significant reduction of syneresis (16.38%), increased the total viable count of starter culture, acetaldehyde and diacetyl contents (167.10 and 18.82 mg/100 g) in yoghurt, followed by banana peel (BP). Stirred yoghurt fortified with BP nano-powder had the highest total phenolic content (20.96 mg gallic acid/g) and DPPH scavenging activity (31.93%) as average values during storage compared to the other nano-fruit wastes. Sensory attributes of stirred yoghurt were improved with the addition of WMR and BP during storage periods, compared to those fortified with AK and PK. All the nano-powders of the studied fruit wastes constitute excellent raw materials for the development of novel functional stirred yoghurt.