This study aimed to demonstrate the feasibility of improving the properties of pea protein isolate (PPI) related to food applications via deamidation with glutaminase. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared (FT-IR) profiling revealed that the current glutaminase treatment did not change the basic protein subunit composition. However, it allowed a certain extent of protein unfolding and conformational reorganization to generate more flexible and extended proteins with reduced average particle size and more hydrophobic groups exposed. The underlying mechanisms might include the reduction of β-sheets and antiparallel β-sheets and the increase of the β-turn structure. Moreover, the treatment time was of importance. A 12 h treatment was generally better than a 24 h treatment, and PPI treated with glutaminase at 50 °C for 12 h to a degree of deamidation of 56.1% exhibited significantly improved solubility, homogeneity, dispersibility, and suspendability with reduced beany flavor, grittiness, and lumpiness (compared to those of the untreated PPI). Thus, the glutaminase treatment offers a promising approach for enhancing the usability and applicability of pea proteins.