As one of the regional Conferences of Mennonite Church USA, the congregations belong to nine Districts: Calvary, Central, Eastern (VA), Harrisonburg, Northern, Potomac, Southern, and Tennessee/Carolina/Kentucky.

Congregations appoint delegates to represent them at two meetings a years to discern issues and vote on resolutions.

The Faith and Life Commission strives to "provide leadership for Conference in spiritual, doctrinal, and faith and life issues, be a forum for interchanging concerns relating to congregational life and leadership, attend to leadership needs of congregations, promote unity of faith and practice, issue ministry credentials, and provide professional development, fellowship and inspiration for pastors,"[4] according to its list of duties.

[5] Virginia Mennonite Conference was in the center of controversy in 2016 when it suspended a pastor in one of its member churches for performing a wedding ceremony between two women.

Pastor Isaac Villegas from Chapel Hill Mennonite Fellowship married the women in May 2016 with the approval of his congregation, and his ministerial license was quickly suspended by VMC with a charge of pastoral misconduct.