Community members said Antwan Haywood, who dresses in drag, is being discriminated against.
A church statement said that Pastor Antonio Rocquemore, of Powerhouse International Ministries, privately warned Haywood on three occasions that dressing like a woman is against church rules.
"During these private sessions the Pastor utilize love, compassion and thoughtfulness in articulating the church policy. The young man agreed to abide by the policy, but would continuously disregard the Pastor's appeal," the statement said.
Haywood said he is in the process of looking for another church.
About 10 people, who were not church parishioners, quietly protested outside the church holding signs against hate speech.