Pea (Pisum sativum L.) proteins are increasingly recognized as favored ingredients in plant-based products due to their excellent nutritional profile, hypoallergenic characteristics, and functional versatility. Thermal processing is crucial for ensuring microbiological safety and extending shelf life. However, heat treatments such as pasteurization and ultra-high-temperature (UHT) processing can denature proteins and compromise techno-functional properties of the final products. Most studies have investigated thermal behavior using purified proteins or protein fractions, overlooking interactions with other proteins and matrix components present in the raw material. Here, we apply a proteomics approach to examine heat-induced changes of proteins using tandem mass tag (TMT)–based LC–MS/MS. Protein extracts were subjected to a wide range of temperature–time combinations (50–95 °C, up to 11 min). Bayesian kinetic modeling was used to estimate kinetic parameters, such as rate constants and activation energies, thereby enabling a detailed characterization of temperature-dependent protein responses. To compile a proteome-wide kinetic profile, we identified 3,127 proteins from yellow pea flour, including 71 well-known pea storage proteins. Kinetic analysis revealed two activation-energy regimes for each pea protein, consistent with reversible unfolding at lower temperatures and irreversible aggregation at higher temperatures. Furthermore, intrinsic protein features, such as amino acid composition, protein size, and structural disorder, were found to be associated with differences in thermal stability across the pea proteome. These findings emphasize the importance of studying protein denaturation within the full protein matrix to more accurately capture the thermal behavior of native proteins. Although complex matrices can complicate the quantification of individual proteins, integrating in-depth proteomic analysis with kinetic modeling provides molecular-level insights into denaturation pathways and their temperature dependence. Overall, this study provides practical guidance for optimizing thermal processing conditions to better preserve the functional properties of proteins in plant-based food applications.