He returned to The New York Times as Washington bureau chief in 2007, after he refused to implement management-desired news room budget cuts at the Los Angeles paper.

[10] Baquet received a scholarship to study English at Columbia University, but dropped out shortly before graduation[11][12][13] to pursue a career in journalism.

Baquet became the top editor in 2005 after Carroll resigned amid clashes with the Tribune Company, which had acquired the Los Angeles Times from the Chandler family in 2000.

[19][26][27] Baquet has made hiring reporters and editors of color a priority, saying that his efforts to diversify the newsroom have been "intense and persistent".

[32] In April 2022, The New York Times announced that Baquet will no longer be executive editor, and will be succeeded by Joseph Kahn.

[33] The New York Times later announced that Baquet would lead a fellowship program to train young journalists in local investigative journalism.

[34] Baquet was awarded the Pulitzer Prize for Investigative Reporting in 1988, in recognition of a six-month investigation that he conducted alongside Chicago Tribune reporters William C. Gaines and Ann Marie Lipinski documenting corruption and influence-peddling in the Chicago City Council in a seven-part series.

Baquet was also a finalist for the 1994 Pulitzer Prize for Investigative Reporting, for stories that exposed "fraud and mismanagement" at the largest U.S. non-profit health insurer.

[36] As managing editor at the Los Angeles Times, Baquet was involved in the newspaper's decision to publish, a few days before the 2003 California recall election, an article containing "a half-dozen credible allegations by women in the movie industry" that Arnold Schwarzenegger, a front-runner in the election, had sexually harassed them.

[37][38] In 2006, Brian Ross and Vic Walter of ABC News reported that Baquet and Los Angeles Times managing editor Douglas Frantz had made the decision to kill a planned Times story about NSA warrantless surveillance of Americans, acceding to a request made to them by the Director of National Intelligence John Negroponte and Director of the NSA Michael Hayden.

In the aftermath of the 2016 U.S. presidential election, Baquet explained to NPR that some mainstream media outlets were too secular for their own good.

[46] The next month, The New York Times published personal details about the whistleblower at the center of the impeachment inquiry against Donald Trump, a decision which Baquet defended.