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Pulse proteins, such as pea and chickpea proteins, have inferior functionality, specifically gelation, compared to soy protein, hindering their applications in different food products, such as meat analogs. To close the functionality gap, protein polymerization via targeted modification can be pursued. Accordingly, transglutaminase-induced polymerization was evaluated in pea protein isolate (PPI) and chickpea protein isolate (ChPI) to improve their functionality. The PPI and ChPI were produced following a scaled-up salt extraction coupled with ultrafiltration (SE-UF) process. Transglutaminase (TGase)-modified PPI and ChPI were evaluated in comparison to unmodified counterparts and to commercial protein ingredients. Protein denaturation and polymerization were observed in the TG PPI and TG ChPI. In addition, the TGase modification led to the formation of intermolecular β-sheet and β-turn structures that contributed to an increase in high-molecular-weight polymers, which, in turn, significantly improved the gel strength. The TG ChPI had a significantly higher gel strength but a lower emulsification capacity than the TG PPI. These results demonstrated the impact of the inherent differences in the protein fractions on the functional behavior among species. For the first time, the functional behavior of the PPI and ChPI, produced on a pilot scale under mild processing conditions, was comprehensively evaluated as impacted by the TGase-induced structural changes.