Both polyphenols and probiotics have beneficial effects on the human body, so it might be beneficial to develop new functional-enhanced food products containing both components. This study investigated the interactions between pomegranate peel polyphenols and Lactobacillus (L.) acidophilus in milk fermentation. There was no inhibitory effect of pomegranate peel extract (PPE) on the growth of L. acidophilus, suggesting that PPE at < 2% (w/v) did not affect cell viability during milk fermentation. On the other hand, total phenolic content and antioxidant capacity in the hydrophilic fraction of fermented milk increased after L. acidophilus fermentation, likely due to the effects of the fermentation. Meanwhile, 13 different phenolic compounds were identified based on LC-MS/MS analysis in L. acidophilus-fermented milk fortified with PPE. L. acidophilus and polyphenolic extracts could co-exist in the same food system with enhanced antioxidant capacity. Hence, it might be feasible to develop new polyphenol-enriched food products, such as fermented milk to provide enhanced health benefits.