Functional proteins such as food enzymes, flavor-enhancing proteins, pigment proteins and milk proteins have been widely used in food processing industry. By improving food texture, enhancing flavor, imparting color, or boosting nutritional value, these proteins increased the added value of food products. However, general issues for the production of these functional food proteins were low synthesis efficiency and higher costs. Microbial cell factories constructed by synthetic biology technologies offered a green and efficient biomanufacturing approach, enabling the high-yield synthesis of various functional food proteins from low-cost biomass feedstocks. Focusing on four representative categories of functional food proteins, food enzymes, flavor-enhancing proteins, pigment proteins, and milk proteins, this review provided a detailed overview of their specific applications and contributions in improving food texture, flavor, appearance, and nutrition. Based on this, recent research progress, key technological breakthroughs, and the current development status of functional food protein biomanufacturing driven by synthetic biology and other advanced technologies were systematically summarized. Finally, the future opportunities and challenges in the field of functional food protein biomanufacturing were reviewed. This review aimed to deepen understanding of biomanufacturing technologies for functional food proteins and to provide valuable insights for fostering continued innovation and industrialization in this domain.