Prosecutors unsealed an indictment charging Wills with 12 counts, including fraud, theft and grand larceny.
Much of the case against him is believed to involve New York 4 Life. In his council bio, Wills describes the group as an "organization which has helped single mothers champion critical issues such as civic literacy and financial empowerment.”
The New York Daily News reported in 2012 that state Attorney General Eric Schneiderman was investigating what happened to a $33,000 state grant to the group.
A member of Wills' staff has also been charged.
Wills, who represents a district in Queens, is a former union employee and political staffer. He was first elected in 2010 after the death of Thomas White Jr., White defeated Wills in the Democratic primary a year earlier.