The governance of the National Alliance for Food Safety will be accomplished by a Board of Directors comprised of one representative from each of the member universities and the Agricultural Research Service (ARS). The Board's routine business will be conducted by an elected Operations Committee consisting of three scientists, three administrators (one designated for an 1890 institution), one representative of the Secretariat, and the administrator of ARS or a designee (invited). The Board will accomplish its objectives through the appointment of subcommittees and task forces as necessary to achieve the stated goal and objectives. USDA agencies, such as ARS, will participate as members of the Alliance. The Board will meet on a annual basis.
The NAFSS functions as a virtual organization with rotating sites for operations and administrative support. Initially, the University of Arkansas housed the Secretariat, but in January 2001 was moved to the Texas Agricultural Experiment Station, a member of the Texas A&M University System.