Metanoia Ministries has served churches in various denominations throughout North America, including the following church affiliation/denomination:
- Adventist
- American Baptist
- Assembly of God
- Baptist General Conference
- Bible Church (Independent)
- Brethren Church
- Christian and Missionary Alliance
- Christian Church
- Church of God
- Conference of Congregational Churches
- Congregational
- Conservative Baptist
- Conservative Congregational Christian Conference
- Covenant Church
- Evangelical Free Church
- Evangelical Friends Church
- Evangelical Lutheran Church of America
- Fellowship of Evangelical Baptist
- Lutheran Churches in Mission for Christ
- Missionary Church
- Non-denominational
- North American Baptist
- Presbyterian Church, USA
- Reformed Church of America
- Southern Baptist
- United Church of Christ
- United Methodist Church
- Wesleyan Church
- Willow Creek Association
