In delivering gradate programming the Graduate School holds an affiliation agreement with Mennonite Brethren Biblical Seminary, and maintains partnerships with Anabaptist Mennonite Biblical Seminary and Steinbach Bible College. It also works in cooperation with the United Centre for Theological Studies at the University of Winnipeg.

A number of Mennonite Churches have an advisory role at the Graduate School through the Winnipeg Centre for Ministry Studies. These churches include the Chortitzer Mennonite Conference, the Evangelical Mennonite Conference, the Evangelical Mennonite Missionary Conference, the Mennonite Brethren Church of Manitoba, and Mennonite Church Manitoba.