Various religious societies have established seminaries at the Faculty of Religion and Theology. They provide an academic education from within the religious background of their own denomination. The following seminaries are at present based in the Faculty: the Baptist Seminary, the Restored Reformed Seminary, the Arminian seminary, the International Baptist Theological Study Centre and the Amsterdam Centre for Orthodox Theology (ACOT).

Most seminaries provide programmes from the degree of Bachelor of Theology to prepare students to the master's level. A number of the seminaries provide post-master training in order to train clergy and chaplains.