In a Presbyterian form of church government, the local responsibility for leading the congregation and overseeing its spiritual welfare rests with the elders of the church (I Timothy 3:1-7). At Heritage Church there are four ruling elders (Rob Amsler, John Boryschuk, Bill Brownfield, and Kevin Horn) and two teaching elders (Steve Hohenberger and Larry Yeager). These six men form the "Session" which is the official governing body of a local church in the Presbyterian Church in America's form of government.

In addition to the Session, a Board of Deacons exists to minister to the physical needs of the congregation and of others whom the congregation has opportunity to serve.

Beyond the local church, all the PCA congregations in a given geographic region form a regional church which is governed by its Presbytery (made up of elders from all of the PCA churches in that geographic area.) On a national level, the denomination is governed by a similar gathering of elders representing all the Presbyteries and churches. They meet annually in a General Assembly.