AbstractConsumers’ preference to have a healthy eating pattern has led to an increasing demand for more nutrient‐dense and healthier plant‐based foods. Pulse proteins are exceptional quality ingredients with potential nutritional benefits, and might act as health‐promoting agents for addressing the new‐generation foods. However, the utilization of pulse protein in foods has been hampered by its relatively poor functionality and unpleasant flavor. Protein structure modification has been proved to be a useful means to improve the functionality and flavor profile of pulse protein. This paper begins with a brief introduction of hierarchical structure of pulse protein materials to better understand the structure characteristics. A comprehensive review is presented on the current techniques including chemical and enzymatic modifications and molecular breeding on pulse protein structure and functionality/flavor. The mechanism and the limitations and the toxicological concerns of these approaches are discussed. We conclude that understanding protein structure‒functionality relationship is extremely valuable in tailoring proteins for specific functional outcomes and expanding the availability of pulse proteins. Furthermore, selective protein modification is a valuable in‐depth toolkit for generating novel protein constructs with preferable functional attributes and flavor profiles. Innovative structure modification with special focus on the molecular basis for the exquisite protein designs is a pillar of pulse protein access to the desired functionality.