The Emma Mennonite Church (named after the Emma community in Lagrange County, Indiana) began in 1901 as an outpost of the Shore Mennonite Church of Shipshewana. Rudy E. Hostetler sold land to the Mennonite Church of Emma on April 8, 1901. The congregation built a meetinghouse the same year. The church began a Sunday school in 1902 and Young People's Bible Meetings in 1903. A sewing circle began in 1918.

The congregation added a basement to the meetinghouse in 1926 and built an annex in 1949. The Emma Mennonite Church established an outpost in Plato, east of Lagrange, in 1948, and  purchased land and built a meetinghouse at that time. In 2001, the congregation began to support Menno-Clinic, a health clinic in Chilivuru, India under the direction of member Doc Yarlagadda. In 2007, it added an eye/dental clinic at Menno-Clinic. Emma Church Park is a 1-acre public park across the street from Emma Church and offers a local playground and meeting pavillion for the community.

In 2016/17, Emma Mennonite Church left the Indiana-Michigan Mennonite Conference. This move was part of a larger realignment of many Mennonite congregations in the 2010s that were formerly part of Mennonite Church USA. These congregations were exasperated by Mennonite Church USA's failure to take stronger disciplinary actions against area conferences and congregations that expressed openness to the inclusion of lesbian, gay, bisexual, and transgender persons in membership and congregational authority. With many other area churches, the Emma Mennonite congregation became part of the Evana Network and subsequently changed its name to Emma Church- An Anabaptist Fellowship.

While Emma has served its local community for nearly 125 years (though very few from the beginning are still with us) and dearly treasures its Anabaptist root system and values, today's congregation is not afraid of embracing modern strategies and methods for advancing the Kingdom of God. Nearly all programs and initiatives of the church are championed by different lay leaders who all serve joyfully. Beside the local church, our congregation is also both financially and relationally loyal to global missionary and outreach endeavors including the above mentioned Menno Clinic in India, Solid Rock Ministries in the Dominican Republic, local social service outposts like food/clothes banks or crisis pregnancy aid, and many individual missionaries. Emma Church is eagerly and prayerfully walking into its next chapters of story bearing witness for Jesus Christ in today's world.