Tuesday's indictment on seven counts of wire fraud alleges Kenneth Terrell, 46, stole the church's money for his own use over a span of four years, said James D. Durham, first assistant U.S. attorney.
Edward J. Tarver, the U.S. attorney for the Southern District of Georgia, said Terrell used his position within the church to steal the money.
"The indictment alleges that Terrell systematically took money over the last four years and used it to support a lavish lifestyle," Tarver said.
The indictment arose from a joint investigation by United States Secret Service Agent William Griffin and Savannah-Chatham detective Raymond Woodberry, Durham said.
Terrell faces a maximum sentence of 20 years in prison and up to a $200,000 fine if convicted.
He also faces child molestation and sexual battery charges in Effingham County.
In January 2010, Effingham County sheriff's deputies arrested him at the church, in the 100 block of U.S. 80, on those charges that stem from events that allegedly occurred between August and October 2009.
David Ehsanipoor, Effingham County Sheriff's Office spokesman, said the victim in that case is from Effingham County and attended the church with his family.
Court documents show that case is awaiting trial.
Terrell has faced a number of other previous charges.
Since 1983, Ehsanipoor said, Terrell, a convicted felon, has been charged with multiple DUIs - including habitual violator - two counts of burglary, forgery, criminal trespass, obstruction, disorderly conduct and drug charges.
He was also charged with child molestation in 1985.