Lyons, president of the National Baptist Convention USA Inc., made arrangements to surrender for an afternoon court appearance before a U.S. magistrate.
He was named in 56 counts carrying a maximum of 815 years in prison and $25 million in fines if convicted.
These allegations come on top of accusations of racketeering and grand theft brought by state prosecutors in February. Lyons, 55, has pleaded innocent to the state counts.
Indicted with Lyons Thursday were Bernice Edwards, 40, former director of public relations for the convention, and Brenda Harris, who was director of meetings and conventions for the Baptist group.
Edwards, a convicted embezzler from Milwaukee, was named in 25 counts; Harris, on eight.
Edwards also faces state charges of racketeering and, like Lyons, has pleaded innocent.
The indictment accuses the three of conspiracy, bank, mail, and wire fraud, making false statements to financial institution and the U.S. Department of Housing and Urban Development, money laundering, interstate transportation of security obtained by fraud, and use of false Social Security number.
In announcing the indictment, U.S. Attorney Charles R. Wilson said he believes that the majority of Baptists would be "sickened and disgusted by the conduct alleged...and are cheering the return of this indictment."