From its inception, Partners has been loosely organized. It operates under the guidance of a Steering Committee made up of representatives of all of the partner groups.

Partners has its administrative home in the Department of Religious Studies, which provides leadership, staff support, and an institutional setting for many of its meetings and conferences. In addition, the Department maintains an Interfaith Fund in the University of South Carolina Educational Foundation which receives tax-deductible contributions for the operation of the Partners program.

Individual contributions and conference fees are the primary sources of Partners funds. Occasionally a faith community makes a contribution of a few hundred dollars to support certain activities. The South Carolina Conference of the United Methodist Church, through its Commission on Christian Unity and Interreligious Concerns, has written Partners' annual interfaith conference into their budget, providing support for promoting the conference among United Methodist clergy and lay people.

Partners prospers because of the dedication of its large company of volunteers. No one is paid to work for Partners. The only exception is that the Graduate Assistants who are assigned to help with Partners activities are paid an assistantship stipend from the Department's operating budget.