Background: Food waste is a global and growing problem that is gaining traction due to its environmental, ethical, social, and economic repercussions. Between 2022 and 2027, the worldwide papaya market is expected to have a huge increase, meaning a growth in organic waste, including peels and seeds. Thus, this study evaluated the potential use of peels and seeds of two mature papaya fruits as a source of bioactive compounds, converting these by-products into value-added products. Proximate analysis (AOAC methods), mineral content (ICP-MS), free sugars (HPLC-ELSD), fatty acid composition (GC-FID), vitamin E profile (HPLC-DAD-FLD), and antioxidant activity (DPPH and FRAP assays) were evaluated. Results: Both by-products showed high total protein (20–27%), and dietary fiber (32–38%) contents. Papaya peels presented a high ash content (14–16%), indicating a potential application as a mineral source. 14 fatty acids were detected, with α-linolenic acid (30%) as the most abundant in the peels and oleic acid (74%) in the seeds. Both by-products showed high antioxidant activity. Conclusion: Papaya by-products display great potential for industrial recovery and application, such as formulation of new functional food ingredients.
