The man, Jay Scott Ballinger, faces at least 42 years in prison, following a plea agreement with the US Justice Department.
Officials said he travelled around claiming to be a missionary of Satan, and would set fire to isolated churches at night as part of his campaign against organised Christian religion.
About 900 places of worship have been burned down across the United States since President Bill Clinton formed a special task force to investigate church arson in 1996.
Pact with the devil
Ballinger's arrest in 1999 was a significant breakthrough for the National Church Action Task Force.
Although it has arrested more than 300 people in connection with more than 200 arsons or bombings between 1995 and October 1999, none have approached the scale of Ballinger's case.
It was widely acknowledged as by far the largest known number of arsons attributed to one person of group of people.
Ballinger, 36, was arrested in February 1999 after seeking treatment at a hospital for severe burns. Satanic books and writings were recovered from his home.
The Justice Department said Ballinger signed individuals he met to contracts with the devil.
Severe burns
At the time, Ballinger admitted to starting as many as 50 church fires in 11 states.
He still faces federal charges in Georgia for starting five church fires in 1998 and 1999, including one in which a fire-fighter was killed.
His 24-year-old girlfriend, who has been charged in connection with one of the blazes, allegedly admitted that she wrote satanic symbols on a church porch before Ballinger set it alight.
She began travelling with Ballinger in 1993 and worked as a night-club dancer to pay their living expenses.
Ballinger is reported to have suffered severe burns over 35% to 40% of his body in a fire in February. He has undergone four skin grafts and is being held at a US medical centre for prisoners.
Southern churches
Legal proceedings against him were put on hold until he was well enough to stand trial.
Many of the blazes dealt with by the National Church Action Task Force have focused on racist motivations, given the high number of attacks against African-American churches in the south.
But the group said in the case of Ballinger, the burned churches in Indiana and Georgia were in predominantly white rural communities.