Methodism in Waycross was growing in the late 1880s and the need for two Methodist churches was evident. Trinity Church was organized as a mission out of Waycross FUMC. In 1893, it was decided to move the church to a new location and, under the leadership of Rev. George Matthews, it moved to the present location. In 1900, a red brick building was constructed facing Church Street. The Woman's Missionary Society was formed in 1896, by Mrs. S. W. Hitch. Mrs. E. M. Cason was the first president.
In the mid-1920s, a youth hut was built and a tabernacle for revivals was constructed at the end of the block on State Street. Later, this would be removed and an annex built in its place. In 1954, the present building began construction to the left of the former building on the site of the old, brown parsonage.
In the early years, the Sunday Morning Love Feast, when members told each other with shouting and singing of the love in their souls and what the Lord had done for them, inspired Frank L. Stanton to write his poem "Love Feast at Waycross." Trinity was one of the last churches in the south to do away with this old-fashioned practice. Trinity is the first in this area to broadcast its services on the radio, first to celebrate Homecoming Day, first to mother two Sunday school classes which grew into churches and the first to have Sunday school classes broadcast their lessons each Sunday.