In 1801 funds were raised to support the building of a place of worship for local Methodists. On January 16, 1802, church trustees purchased land here "on a rising ground beautifully situated for that purpose." A frame chapel was erected soon thereafter and given the name Goshen. The building remained in use until 1879, when a new church on Federal Street was completed. The old meeting house was sold the following year and moved to another location. Land where the building once stood became part of the cemetery.
On November 12, 1817, the trustees of the Milton Academy purchased land on the west side of the church lot on which to build a school. For many years the Academy enjoyed a distinguished reputation for scholastic excellence. It was closed circa 1880. In 1894 the Academy lot was conveyed to the Public School Commissioners of Milton. A two-story frame building was then constructed on the site. Milton's first "high school" remained in used until 1933, when it was replaced by a new facility at another location.
Following the construction of the church a cemetery was established on the grounds. For many years it served as the chief burial place for the residents of the community. Growing concern about the maintenance of the property resulted in the formation of the Milton Cemetery Improvement Company in 1928. Responsibility for the cemetery was transferred to the corporation by the church. In 1966 the lot where the school buildings had stood was purchased for cemetery expansion. Notable burials include those of David Hazzard, Governor of Delaware 1830-1833, and James Ponder, Governor of Delaware 1871-1875.