In 1981, the Nicholls Hospital was torn down and was replaced by a new dorm residence for men and women.

Master's Seminary originated in 1996 as Canadian Pentecostal Seminary (CPS), which was an initiative of the national office of the PAOC to provide training within a Pentecostal context for those with a university degree who were preparing for ministry.

However, this model would not last long due to disagreement about whether campuses should be governed nationally or regionally.

The merged institution was renamed Master's College and Seminary on June 29, 2001.

In the summer of 2010, MCS moved back to Peterborough, becoming the anchor tenant in the same buildings which had previously been sold.