The first church was planted on 4 June 1995 after receiving government approval on 15 May. The first church started in Mungwa, Gitega province, and was named Eglise Manne du Salut (EMS). In March 2005, the organization changed its name to African Methodist Episcopal Church, and became a part of this larger denomination.

The founders of AMEC Burundi are two pastors, Rev. Marc Nzikobari and Pastor Zacharie Mpawenayo. The first church plants were in Mungwa and Songa. Today, with the Village Church Planting Program (VCP), the group is planting many churches in different provinces of Burundi. In its association with the Into Africa Project, AMEC has planted hundreds of churches with thousands of members. As of June 2011, 322 churches with 9,234 members were a part of the denomination itself.