The conference was formed in 1860 by congregations in Iowa seeking to unite with like-minded Mennonites to pursue common goals such as higher education and mission work.

The merger was "finalized" at a joint session in St. Louis, Missouri, in 1999, and the Canadian branch moved quickly ahead.

The United States branch did not complete their organization until the meeting in Nashville, Tennessee, in 2001, which became effective February 1, 2002.

The Alliance of Mennonite Evangelical Congregations represents one expression of the disappointment with the merger and the events that led up to it.

[3] This decline was is generally attributed to the denomination's increasingly liberal position towards same sex marriage, among other issues, which caused many congregations to leave Mennonite Church USA.

Delegates from local congregations, regional area conferences, and constituency groups gather to develop vision and direction for the national denomination.

Previous conventions have been held in Nashville, Tennessee (2001), Atlanta, Georgia (2003), Charlotte, North Carolina (2005), San Jose, California (2007), Columbus, Ohio (2009),[12] Pittsburgh, Pennsylvania (2011), Phoenix, Arizona (2013), Kansas City, Missouri (2015, 2019, 2021, 2023),[13] and Orlando, Florida (2017).

Recently, some divisions have occurred and the Lancaster Conference (not included here) voted in 2015 to leave the Mennonite Church U.S.A. by 2017.

MEA also helps bring support and leadership to Mennonite colleges, universities, and seminaries located throughout the United States.

It contains 24 articles ranging from the more general Christian theologies of God, Jesus Christ, and the Holy Spirit to the more distinct Foot Washing; Truth and the Avoidance of Oaths, Peace, Justice, and Nonresistance; and The Church's Relation to Government and Society.

The Brethren Mennonite Council has been active since 1976 to encourage "full inclusion" for lesbian, gay, bisexual, and transgender persons in the church.

In 1987, the Mennonite Church (another predecessor of MC USA) issued the Purdue Statement, with similar language.

[40] In 2015 discussions revolved around the decision by multiple conferences to license openly LGBT members for church ministry.

[41] Due to the denomination's increasingly liberal position, the Lancaster Conference voted in November 2015 to leave the Mennonite Church USA.

[8] At the same time, toward the end of 2015, the Western District Conference voted to allow ordained ministers to officiate at and perform same-gender marriages.