The origins of this congregation date to 1870, when circuit-riding ministers visited people living along the Colorado River at Red Bluff. Norman Savage (1826-1879), a church elder, served the small congregation, and the first minister was Thomas W. Rogers.
When the town of Bay City was surveyed in 1894 the Methodist congregation relocated and bought one of the first town lots. By 1897 they had built Bay City's first church structure, a frame building with a steeple and bell. The building also served as a Union church for other denominations in the town.
The congregation purchased land at Fourth Street and Avenue H in 1904, and the original church building was later sold to the Bay City school system. Services were held in the courthouse and a building on the square until a temporary open-air tabernacle was built. Additional land was acquired in 1906, and a new sanctuary was completed in 1909 during the pastorate of A. S. Whitehurst. The church's fifth building was erected in 1958 and dedicated on March 30 of that year. A part of Bay City and Matagorda county history for over a century, the Bay City Methodist Church continues to serve the community.