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The aim of the current study was to evaluate the effect of apple peel polyphenol extract (APPE) on the physicochemical and microbiological properties of probiotic yoghurt. Five concentrations of APPE were added in probiotic yoghurt as: (1) CTL, control without APPE; (2) AE1, addition of 1% APPE; (3) AE2, addition of 2% APPE; (4) AE3, addition of 3% APPE; (5) AE4, addition of 4% APPE; and (6) AE5, addition of 5% APPE. The prepared probiotic yoghurt was stored at 4 °C for 21 days and analyzed for physicochemical and microbiological properties. The initial viable count of L. bulgaricus, S. thermophilus, B. lactis and L. acidophilus were similar in all yoghurt samples at day 1. The maximum viability loss of probiotics was observed in CTL (p < 0.05). The lowest viability loss of probiotics was observed in AE5 samples (p < 0.05). The acidity, water holding capacity and viscosity were increased with the addition of APPE. No significant effects were observed on milk fat and total solid contents of probiotic yoghurt with the addition of APPE. The total phenolic contents of probiotic yoghurt increased significantly as 0.59, 0.71, 0.97, 1.18, 1.35 in AE1, AE2, AE3, AE4 and AE5, samples respectively. It was observed that AE3 and AE4 samples had better taste, flavour and colour with good texture. The survival of probiotics and antioxidant activity of the yoghurts were enhanced with the addition of APPE. In conclusion, apple peels could be successfully used as prebiotic in yoghurt with increased viable counts of probiotics.