In 1860 a mission was established in Gainesville meeting in private homes. Trinity Parish was organized in 1868 with twenty-six communicants. Services were held in the Courthouse and later the Town Hall. In 1873 a small frame Carpenter Gothic Church was built on the corner of North Main and Northeast Second Avenue. Incorporated in 1886, the name was changed to Holy Trinity.

In 1903 the present church property at the corner of Northeast First Street and First Avenue was bought, and when the church was completed in 1907, it served about 100 communicates; including sixteen stained glass windows; oak reredos hand-carved by artists from Oberrammergau, Germany; altar and a brass eagle lectern. A parish hall with classrooms was built in 1923, and the Phillips Education building was added in 1961.

When the 1907 church building was destroyed by fire on January 21, 1991, it was mourned by all of Gainesville. A second fire in 1992 destroyed the 1923 Parish hall. The rebuilding process was started immediately to replace and expand the church and facilities.

The entrance tower and church bell survived the fire, and the brass eagle lectern was recovered and restored. Composite stone from the destroyed church building was salvaged by members of the parish and used for the courtyard fence.

The continuing presence of Holy Trinity in the downtown area for more than 100 years has been a source of comfort and hope for many and a visible sign of God's love.