David Lopez Jackson has been charged over the fires at Ebenezer Lutheran Church and New Life Missionary Baptist Church in St Louis, Missouri in October.
Mr Jackson remains a suspect for the other five October church arsons in Missouri, but has not yet been charged in connection with them.
The attacks were originally thought to be racially-motivated, with five of the seven churches being predominantly African-American, however authorities have now said this is not the case.
The American Bureau of Alcohol, Tobacco, Firearms and Explosives said in a statement: "Based on the investigation so far, there appears to be no indication of a hate crime or sign of any one particular Christian denomination or ethnic group being targeted."
Church leaders have expressed relief that the arsons were not racially motivated, and hope that the perpetrator receives appropriate help.
Missouri has had a long history of racial tension as a southern US state, which was reignited when unarmed black teenager Michael Brown was shot dead by a white policeman in 2014.
A jury then decided not to charge the policeman, Darren Brown.
