Thomas Galante, who makes $392,000 a year, will continue to receive his salary and benefits, the library said.
The board also decided Thursday to provide City Comptroller Scott Stringer with all of the library's financial documents, which the trustees had initially refused to do.
“My audit will seek to tell the full story behind what has been a sordid series of reports of alleged poor governance and irresponsible spending at the Queens Library,” Stringer said in a statement.
The board selected Bridget Quinn-Carey, the current executive vice president and COO, to serve as interim president and CEO.
“Tonight's decision by the board is part of its ongoing efforts to [e]nsure the public that the Library's actions are being conducted in an open and transparent manner," library officials said in a statement.
The library added that it will “investigate opportunities to resolve the current dispute through mutual agreement.”
Galante, who has served as the library's president and CEO for more than a decade, was criticized for his salary and spending, including $140,000 for renovating his office at the library's main branch in Jamaica.
He also came under fire for holding a second $114,000 job as a consultant, according to published reports.
A number of elected officials, including Queens Borough President Melinda Katz, have called for Galante’s resignation.
But Galante had been able to maintain the support of the majority of the board, which in April voted to retain him.
After Gov. Andrew Cuomo signed a bill in June to reform the Queens Library, making it easier to remove library trustees, Katz and Mayor Bill de Blasio dismissed eight board members and nominated newcomers — who supported putting Galante on administrative leave.
A spokeswoman for the Queens Library said Friday that the terms of Galante's leave precluded her from contacting him.
Information about Galante's lawyer was not immediately available.