During Michael D. Jones's principalship, a row broke out between two rival factions within Welsh congregationalism over the seminary's constitution – Michael D. Jones and his followers wanted to keep and adhere to the old constitution but Rev.
John Thomas of Liverpool and his followers wanted to impose a new constitution upon the seminary.
John Thomas's plan would only lead to the presbyterizing of the seminary and of the Congregational churches in general.
The seminary remained in Bangor until its closure in 1989 by which time it was under the principalship of R. Tudur Jones, the last in the distinguished line of Principals to serve the Congregational churches in Wales.
Through the 1990s, the United College remained at Aberystwyth, until its closure – now Congregational training is based back in Bangor under the supervision of Rev.