
White church leaders were dismayed at the growth in African American membership, which soon surpassed the segregated seating available. When Allen and fellow preacher Absalom Jones were asked to move during prayer while sitting in a whites-only area, they left St. George's and formed the Free Africa Society (FAS), a non-denominational mutual aid society. The FAS became primarily affiliated with the Episcopal Church, but Allen remained Methodist, saying "I was confident that there was no religious sect or denomination would suit the capacity of the colored people as well as the Methodist; for the plain and simple gospel suits best for any people."
He then founded Mother Bethel AME, originally affiliated with the MEC, but in 1816 met with leaders of other African American congregations to form the AME and was elected its first bishop. Read more about the AME here http://ame-church.com/our-church/our-history/