The pequi (Caryocar brasiliense) fruit peel, despite being frequently discarded, has a high content of bioactive compounds, and therefore has a high nutritional value. The present study aimed to explore the bioactivities in the pequi peel, particularly their potential health benefits at the level of antioxidant activity. The exploitation of this fruit could also present significant economic benefits and applications of pequi by-products would represent a reduction in waste, having a positive impact on the environment. Phenolic compounds present in the pequi exocarp and external mesocarp were identified by paper spray mass spectrometry (PS-MS) and quantified by HPLC. The total phenolic content (TPC) along with the amount of 2,2-diphenyl-1-picrylhydrazyl (DPPH), Ferric Reducing Antioxidant Power (FRAP), and the amount of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid (ABTS) were also determined in peel extracts. Epicatechin was the most abundant phenolic compound found, followed by the caffeic, salicylic, and gallic acids. In addition, fingerprinting revealed compounds related to several beneficial health effects. In short, the results obtained were encouraging for potential applications of pequi peel in the field of functional foods.