Correction: An earlier version of this story stated that Bill Keller became the executive editor of the Times before the U.S.-led invasion of Iraq in 2003. He assumed that role four months later.

Bill Keller, the New York Times’ former executive editor and current columnist, will leave the paper after three decades to head a nonprofit news organization, the newspaper said Sunday.

Keller, 65, will become editor-in-chief of the Marshall Project, a start-up operation that will specialize in criminal-justice reporting.

Keller was editor in chief of the Times from 2003 to 2011. He became executive editor four months after the U.S. military invasion of Iraq in 2003. The Times later acknowledged that its reporting on this period — particularly on the existence of weapons of mass destruction in Iraq — was flawed.

Under Keller’s editorship, the Times published excerpts of sensitive U.S. military and diplomatic files obtained by WikiLeaks, the anti-secrecy organization that had received them from then-Army Pvt. Bradley Manning. The paper also published stories disclosing the George W. Bush administration’s practice of “warrantless wiretapping” of suspected terrorists in 2005.

The Times won 18 Pulitzer Prizes during Keller’s eight-year tenure.

Years earlier, as the Times’ correspondent in Moscow, Keller won a Pulitzer Prize for international reporting in 1989. He also reported from South Africa during the period in the early 1990s when the country’s apartheid racial laws began to erode and Nelson Mandela became the nation’s president.

He has been a columnist at the Times since stepping down as editor. He and his wife, Emma Gilbey Keller, stirred controversy last month when they both wrote columns critical of a cancer patient, Lisa Bonchek Adams, who had blogged and tweeted about her illness. Keller wrote his column for the Times; his wife wrote hers several days earlier for the Guardian newspaper. Both drew criticism from Adams, among others.

The Marshall Project is a nonpartisan, nonprofit organization that is still being formed. It was started by Neil Barsky, a former Wall Street Journal reporter who became a successful hedge-fund manager. The project is one of a number of digital-only news organizations that have formed in recent years outside of traditional media companies.

Arthur Sulzberger Jr., the Times’ publisher and chief executive of its parent company, said in a statement to the paper: “Bill has made so many contributions to the Times over his 30 years here, it’s difficult to quantify them. He challenged his newsroom colleagues to innovate while remaining true to the highest journalistic standards, and we’re all better for it.”