The Bergthaler Mennonite Church of Manitoba traces its origin to the ordination of Johann Funk in 1882 (although the church did not subscribe to the Bergthaler name until 1892. Funk led the Mennonite people who had migrated from the Manitoba Mennonite East Reserve since 1877. These people settled on the east side of the West Reserve in what is now the Altona-Gretna area. Originally these people had immigrated to Canada from the Bergthal and other colonies in Russia. In the East Reserve their church became known as the Chortitzer Mennonitengemeinde. In 1889 the Choritizer church gave their members on the West Reserve more autonomy with the establishment of the Waisenamt (church mutual aid institution). Johann Funk pushed the church into new territory with the vision of a teacher-training center in 1885. This became a reality in 1889 with the establishment of the Mennonite Educational Institute (MEI) later known as the Mennonite Collegiate Institute (MCI) in Gretna, Manitoba. Funk also proposed to have singing practices, Bible studies, Sunday School and fellowship with other churches. The biggest issue became education and the continuation of the MEI. The parent church on the East Reserve did not support Funk and in 1892 a church split occurred. A group of fifty-seven to sixty-one families chose to side with Funk but the vast majority, 441 families aligned themselves with the parent church. A new bishop, Abraham Doerksen from the village of Sommerfeld, was elected by the Chortitzer church in 1894 to serve its members. This larger group became known as the Sommerfelder Mennonite church and Funk's group as the Bergthaler Mennonite church. Included in Funk's small group of supporters were a few ministers. One of these, Jacob Hoeppner, was elected as an assistant to Funk in 1903. In that same year the Bergthaler church formed a partnership with the Rosenorter Mennonite church of Saskatchewan, beginning what became the Conference of Mennonites in Canada. In 1926 David Schultz was elected as the Aeltester (Bishop) to take over the responsibilities from Hoeppner. During this era the church expanded greatly due to the depression forcing people to move, the influx of new Mennonite immigrants and the controversy over the school and Waisenamt having somewhat been forgotten.
A finance commmittee was organized in 1929, taking control of finances away from the ministers. Other new venture in subsequent years included the establishment of the Elim Bible School, Mennonite Pioneer Mission to aid Mennonite people in Mexico and native people in Canada, the Christian Home Hour and the Abundant Life radio programs aired on CFAM in Altona, Manitoba. The church established seniors homes and a Christian Bible camp (Moose Lake Camp). It published church paper called Das Bergthaler Gemeinde Blatt printed by D.W. Friesen Printers in Altona, Manitoba. The church also supported its young men with getting contentious objectors (CO) status during World War Two and with visits to the men in the Alternative Service camps.
The church suffered a serious set back when the Waisenamt, where many people had invested their life savings, collapsed in 1931.
When Schultz began as Bishop in 1926, the church had three houses of worship. By 1952 there were ten church buildings, twenty-one places of worship, twenty-four Sunday schools, one Bishop (Aeltester) and twenty ministers. The church began a decentralization process when it began to ordain more elders, moving away from the strong one leader concept. In 1951 J.M. Pauls of Morden, Manitoba was ordained and served until his death in 1961. In 1961 D.D. Klassen and J.F. Pauls were ordained and in 1962 Ernest Wiebe was ordained. In 1965 the Bergthaler church continued to decentralize, giving more autonomy to the local churches. In 1967 ministers in the local churches had the right to baptize and serve communion, which had earlier one been done by the bishop. By 1968 the Bergthaler Mennonite Church of Manitoba had almost totally decentralized with all the major church programs having been assumed by board of the General Conference Mennonite Church or the Conference of Mennonites in Canada. With decentralization almost complete, the next step by default was dissolution. In a meeting in Carman, Manitoba on March 9, 1971, the nineteen congregations decided to dissolve the Bergthaler Mennonite Church. This action became final in 1983 when Bill 112 received Royal Assent and the Act to incorporate the Corporation of the Bergthaler Mennonite Church of Manitoba was repealed.