The eighteen-year-old's death by a police officer has caused riots across the US.
Now the pastor at Flood Christian Centre says the building's been torched but doesn't think those protesting are to blame.
Speaking to NBC News Revd Carlton Lee said he believes the church was targeted because he has continued to call for the arrest of Officer Darren Wilson.
A grand jury ruled that he shouldn't face criminal charges over the death of Michael Brown.
Revd Lee said: "The police called me and told me the church was on fire. I was in complete disbelief. I didn't think anyone would set a church on fire."
"I feel like one of my children has died. I put my blood, my sweat, my tears into this church, getting this church built from the ground up. To see that it was taken down in a few minutes is really heartbreaking."
According to NBC News, Mr Lee claims white supremacists are to blame.