The first churches founded in Augusta county were Presbyterian: Stone Church (or Augusta), Tinkling Spring, Hebron (or Brown's Meeting House), Rock Spring, and Bethel. Mossy Creek was organized in 1767. Staunton's Presbyterians were initially affiliated with Tinkling Spring or Hebron, as were those in Waynesboro. In 1818 Presbyterian Church was erected in Staunton; one was built in Waynesboro in 1847. Later Presbyterian churches in the county included Union (1817), Shemariah (1832), Mt. Carmel (1835), Mt. Horeb (1857) and Lock Willow, built in Churchville in 1866. The Associate Reformed or "Seceder" Presbyterians had their own church, Old Providence.

Augusta also had a significant Episcopal presence, in part because the church was legally established in Virginia until the Revolution. At mid-century there were two Episcopal churches in the county: one at Boyden, 5 miles SE of Staunton, and Trinity Church, in town. Trinity church owned two acres in the center of Staunton, and the Revolutionary War Virginia General Assembly held sessions in the church itself, after being driven from Richmond and Charlottesville.

There were several Lutheran churches in the county. The first, Coiner's, or Trinity, on South River was founded in 1780, followed by Mt Tabor in Riverheads, 1785; Mt. Zion, near Middlebrook, 1830; Mt. Hermon, near Newport, 1850; Bethlehem, near Fishersville, 1843, Mt. Zion, in Waynesboro, 1845; Staunton Lutheran Church, 1850; Salem near Mt. Sidney, 1845; Churchville, 1850. Other Lutheran churches included Bethany and Waynesborough.

Augusta county's Methodists were, according to Joseph Waddell's Annals of Augusta County, too numerous to name. As he explained, "there is now [1880s] a Methodist church at nearly every village in the county, the number of churches and chapels being eighteen, besides several colored Methodist churches". One of the best known churches, in Staunton, gave the "Gospel Hill" area its name.

Augusta had a sizable German population, over a hundred Augustans were born in Germany and many others were second-generation German immigrants. Consequently several German Reformed churches. These included St. John's, New Bethany, and Mint Spring. The Tunkers or German Baptists were also present, and worshiped at Mt. Vernon, Barren Ridge, Valley District, and Moscow.

Other denominations in the county included the United Brethren. A Catholic church was built in Staunton in 1850, and maintained an affiliated school, staffed by the Sisters of Charity. The Baptists also built a church in Staunton during the 1850s. According to Waddell, by the 1880s there were six Baptist churches in the county, and two "colored churches" in Staunton proper. Two of these were Mt. Zion Baptist Church and Augusta Street United Methodist Church.