The Protestant Institute is coordinated by five bishoprics: one Unitarian and two Lutheran, together with the Reformed Piatra Craiului District and Transylvania District. Its Cluj-Napoca center houses two branches — the Reformed-Evangelical Faculty (offering training for members of the Reformed Church and the Evangelical Lutheran Church), and the Unitarian Faculty. In addition to these, the Institute includes a Saxon-Evangelical Faculty, which is based in Sibiu and is maintained by the Evangelical Church of Augustan Confession.
The Institute was founded in 1948, reuniting the Cluj-based Reformed Theological Faculty and Unitarian Faculty the Theological Academy, as well as being the first local seminary for Lutherans. It has a claim to being the sole Protestant theological institution to teach in two languages (Hungarian and German) and to have two separate local sections.