Agro-industrial wastes contain a large number of important active compounds which can justify their use as innovative ingredients in nutraceutical products. This study aimed to provide a complete analysis of active molecules, namely (poly)phenols in pea pods water-based extracts, through a UHPLC-Q-Orbitrap HRMS methodology. Data showed that 5-caffeoylquinic acid, epicatechin, and hesperidin were the most relevant (poly)phenols found in the assayed extracts, with a mean value of 59.87, 29.46, and 19.94 mg/100 g, respectively. Furthermore, changes in antioxidant capacity and bioaccessibility of total phenolic compounds (TPC) after the simulated gastrointestinal (GI) process were performed using spectrophotometric assays (FRAP, DPPH, ABTS, and TPC by Folin-Ciocalteu). The acid-resistant capsules (ARC) and the non-acid resistant capsules (NARC) containing the pea pod extract underwent simulated GI digestion. The results suggested that the ARC formulations were able to preserve the active compounds along the simulated GI process, highlighting a higher TPC value and antioxidant capacity than the NARC formulations and the not-encapsulated extracts. Hence, the pea pods water-based extracts could be utilized as a potential alternative source of active compounds, and the use of ARC could represent a suitable nutraceutical formulation to vehiculate the active compounds, protecting the chemical and bioactive properties of (poly)phenols.