The industrial processing of pineapples generates a substantial quantity of by-products including shell, crown, and core. Bromelain, a proteolytic enzyme found naturally in pineapple including the by-products, may positively influence the bioaccessibility of phenolics from milk coffee. Therefore, this study aimed to assess how the inclusion of pineapple by-products, namely shell, crown and core, could impact the bioaccessibility of coffee phenolics when combined with milk. After measuring the proteolytic activity of pineapple by-products, the standardized in vitro digestion model of INFOGEST was employed to evaluate changes in total phenolic content, total antioxidant capacity, and individual phenolic compounds of different coffee formulations. The results showed that incorporating extracts from the crown or core in both black and milk coffee increased the bioaccessibility of total phenolics and antioxidants (from 93–114% to 105–129% and 54–56% to 84–87%, respectively), while this effect was not observed for the shell. Moreover, adding core extracts also enhanced the bioaccessibility of caffeoylquinic acids and gallic acid in milk coffee (from 0.72–0.85% and 109–155%, respectively). Overall, the findings of this study highlighted that bromelain from pineapple core may have a favorable effect on the recovery of phenolic compounds in milk coffee.