This church, named for Rev. E. F. Morgan, had its beginning in 1925, under the leadership of the Rev. R. F. Owens, who then held the Darien Charge. A site was selected under an oak tree near where the Abraham McIntosh house once stood, and a tabernacle was built with lumber donated by Duke M. McIntosh. Services were held there until the tabernacle burned down. Another lot was then purchased, and a new church building constructed by Daniel Mercer, Raleigh Wallace, and Clarence Hope. Later, it was decided to move the church building to the present site, which had been purchased with funds raised by donation and box suppers served by the members of the church. The new edifice was used until about 1965 when it was torn down and the present church building built by the efforts of Ralph Douglas, Harry Jackson and faithful members of the church
. This building was completed in 1967. Since that time, Sunday school rooms have been added.
In 1993, the church was refurbished including a new altar, choir loft, and a vestibule. In June 2000, Morgan's Chapel became a station church and no longer shared a pastor with Darien UMC. At that time, Rev. Charles Ricks, who had served both Darien and Morgan's Chapel for two years prior, retired and was appointed to be the part-time pastor at Morgan's Chapel. Under Rev. Rick's pastorate, membership continued to increase and a social hall and kitchen were built. The church constructed a parsonage in 2006-2007, and Rev. Devin Schultz became the first full-time pastor.