Pineapple is a tropical fruit consumed fresh or processed into various food products. However, the peel and crown of this fruit are not industrially exploited, thus generating tons of by-products that represent an economic and environmental concern. In order to promote the upcycling of these by-products, this work aimed to characterize the phenolic profile of its hydroethanolic extracts obtained from pineapple peel and crown leaves and to evaluate their in vitro bioactivity. The HPLC-DAD-ESI/MS analysis allowed the identification of 25 phenolic compounds, including phenolic acids and flavonoids. The antioxidant, cytotoxic, and antimicrobial activity assays highlighted the peel extract as the most promising and, therefore, it was incorporated into a traditional Portuguese pastry cake as a functional ingredient. The nutritional parameters of the developed food were not affected by the incorporation of the extract, but it promoted the antioxidant activity during its shelf-life. Overall, pineapple peel and crown appeared as promising by-products to be exploited by the food industry, which can be achieved through a circular economy approach.