On February 5, 1736, Rev. John Wesley landed in Savannah and held regular preaching services on a lot on St. James Square, now Telfair Square, where Trinity would be built. There were preachers assigned to Savannah from the beginning of Methodism in America, but Rev. James Russell was the assigned preacher who built Wesley Chapel, the first Methodist Chapel in Savannah, in 1812-1813. Mr. Russell cut the logs and floated them down the Savannah River and personally went into debt to construct the two-story, wooden building at the corner of Lincoln Street and Oglethorpe Avenue. Bishop Francis Asbury preached in this building and dedicated it. This was the beginning of Trinity and Asbury UMC. When this building grew too small, the congregation decided to relocate, though for a few years a small number remained at Wesley Chapel.
First known as Wesley Chapel, the church known today as Trinity Church is located at 127 Bernard Street, on Telfair Square, formerly St. James Square. The land where the church is located was part of the original city of Savannah and was a Crown Grant from the King of England to William Ewen and John Hamm. The trustees of Wesley Chapel bought it in 1848, in order to erect a sanctuary large enough for their growing congregation. Under the pastorate of A. T. Mann on February 14, 1848, the cornerstone was laid and, in 1850, the membership moved to the new building. Trinity is architecturally in the Greek revival style, similar to the design of Wesley Chapel in London. In 1876, Dr. E. H. Myers, pastor of Trinity, died from yellow fever during an epidemic that hit Savannah. In 1895, Robert McIntire paid for a Sunday school building to be constructed. This building was replaced on February 13, 1927, by a modern, four-story building. A kindergarten was organized in the early 1900s and in 1928 Capt. George P. Walker left an endowment for the program in memory of his mother. In 1967, the sanctuary was renovated, restoring it to the original 1848 design. Trinity has been instrumental in the founding of Wesley Monumental, Epworth, Asbury Memorial, Grace, Aldersgate, Wesley Oak, Robert McIntire, and White Bluff.
In 1991 a fire destroyed the Educational Building. After two years of construction, the building, now named the McIntire Building, was completed in 1993. In 2002 the top floor of the McIntire Building was turned into a 4800 square foot parsonage called the Hendrix House. In 2005 the exterior of the church was restored, winning an Award of Excellence from the Historic Savannah Foundation. In recent years the church hosted various community programs including the Savannah Music Festival and the Savannah Book Festival.