Center for Food and Biomolecules was established on July 12, 1994. The major goal in this center is to organize research teams and promote integrated research projects, as well as the implementation of the commercialization of research results. Professor Wenz-hang Jiang served as director of the center. Zi-ming Pan was a convener of consultative Committee Professor. The Centre was set up for seven divisions: (1) division of traditional food processing technology ,headed by Je-Chiu Yu; (2) division of health functional food research and development, headed by Distinguished Professor Lee-Yan Sheen; ( 3) division of nutrition protein bodies Study, headed by Professor Ning-Xin Xiao; (4) division of nano technology, headed by Professor An-yi Yeh; (5) division of mass production of food and biochemical technology, headed by Cu-Yang Chou; (6 ) equipment and services group, headed by Professor Xu Fu; (7) administrative and Planning group, headed by Professor Ming-ru Chen. The past results included: the completion of a two-stage fermentation to make sauerkraut, which solved the problem of the traditional fermentation production on sauerkraut in Dapi, Yunlin Country. Local nature ingredients such as barley, probiotics, mushroom as well as their health benefits and efficacy marker gene group reaction pathway had been studied. The results of strengthening Innovative R & D counseling case include: NTU refreshing tea (臺大清爽茶), health drinks of enokitake mushroom (金針菇), Nano drinks of Ganoderma (奈米研磨靈芝飲品)and microencapsulation of probiotic(益生菌微膠囊).

On August 4, 2010, the former director, Professor Wen-Zhang Jiang hand the center to the current director, distinguished Professor Lee-Yan Sheen. Professor Sheen reorganized organization structure from seven divisions to four ones: divisions of Functional Food Research, Mass Production Technology, Equipment and Service and Administration. The leader of Functional Food Research division is Prof. Nan-Wei Su. The leader of Mass Production Technology division is Associate Prof. Cu-Yang Chou. The Leader of Equipment and Service division is Prof. Fuu Sheu. The leader of Administration division is Associate Prof. Yi-Chen Lo.

In 2000, the center established the affiliate of International Association for Food Protection (IAFP), which is the 48th international branch of the IAFP. Besides, the center also helped TFDA to found the National Center for Food Safety Education and Research in 2012.