The organization of the Hamburg Methodist Episcopal Church started with the founding of the Genesee Conference in 1810. The New Amsterdam Circuit included Hamburg. In 1813 Reverend Gideon Lanning worked this circuit which stretched from Batavia to Niagara and from Towanda to south of Buffalo. This was later divided into four circuits including the Eden and Hamburg circuits, beginning in 1819. In 1822 a camp meeting at Hamburg was the first activity other than class meetings. In 1839 Brother H.M. Ripley took over the circuit and under his ministry a church of 150 members was built and dedicated that same year under Pastor Amos Worchester. Later in 1858 under R.N. Leeke this church had the largest revival in the vicinity with 400 conversions. In October 1864 the charge was first referred to as the Hamburg Eden charge in the quarterly conference minustes. In October 1866 the Hamburg and Eden charges divided, with Coopers Ridge (after July 29, 1870), Potters Green (services discontinued July 1867), Abbotts Corners, and Whites Corners falling under Hamburg's jurisdiction. Later Water Valley and Town of Armor were included. A new church was started November 10, 1884, which ran into trouble when the contractors refused to complete the work and had to be taken to civil court.

In July 1884 a distinction was further made between the charges of East Hamburg and Hamburg. On January 30, 1886 the Hamburg-Buffalo district of the Genesee Conference was officially recognized. On May 9, 1887 the new church was finally dedicated in Hamburg. The Town of Armor appeared on this charge September 18, 1896 and in 1906 it became the Hamburg-Amor charge, temporarily. Another new building was started on March 2, 1909 and was not completed at the end of the records in 1927. The town of Armor was dropped from the charge on September 14, 1917. On April 2, 1926 the church in Hamburg's name was officially changed from the Second Methodist Church to the Hamburg Methodist Episcopal Church.