Bill Keller, a columnist at The New York Times and its former executive editor, will leave the paper to become editor in chief of The Marshall Project, a nonprofit journalism start-up focused on the American criminal justice system.

“It’s a chance to build something from scratch, which I’ve never done before,” Mr. Keller said, “and to use all the tools that digital technology offers journalists in terms of ways to investigate and to present on a subject that really matters personally.”

Over the course of a three-decade career at The Times, Mr. Keller won a Pulitzer Prize for international reporting as a correspondent in Moscow; chronicled the collapse of apartheid as the paper’s Johannesburg bureau chief; and served as executive editor from 2003 to 2011.

“Bill has made so many contributions to The Times over his 30 years here, it’s difficult to quantify them,” said Arthur O. Sulzberger Jr., publisher of The New York Times. “He challenged his newsroom colleagues to innovate while remaining true to the highest journalistic standards, and we’re all better for it.”