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 its by-products, may positively influence the bioaccessibility of phenolics from milk coffee. Therefore, this study aimed to assess how the inclusion of extracts from 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 in 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 (from 93 to 114% to 105–129%) and antioxidants (from 54 to 56% to 84–87%), 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 to 0.85% and 109–155%, respectively). Overall, the findings of this study highlight that bromelain from pineapple core may have a favorable effect on the recovery of phenolic compounds in milk coffee, possibly due to its ability to cleave proteins. These outcomes point out that industrial by-products can be transformed into economic value by being reintroduced into the production process through suitable treatment instead of disposal.