The first editor of The Sacramento Bee was John Rollin Ridge,[11] but James McClatchy took over the position by the end of the first week.

[13] On March 13, 2006, The McClatchy Company announced its agreement to purchase Knight Ridder, the United States' second-largest chain of daily newspapers.

The purchase price of $4.5 billion in cash and stock gave McClatchy 32 daily newspapers in 29 markets, with a total circulation of 3.3 million.

[5][16] In the fall of 2020, the Bee announced[17] it would be vacating its longtime headquarters and printing plant in Midtown Sacramento at 21st and Q Streets (which it occupied since 1952), citing the need to cut costs and streamline in the wake of declining ad revenues, the rise of online journalism and the impacts of the COVID-19 pandemic, during which most journalists and employees worked from home.

[19] It has won numerous other awards, including many for its progressive public service campaigns promoting free speech (the Bee often criticized government policy, and uncovered many scandals hurting Californians), anti-racism (The Bee supported the Union during the American Civil War and publicly denounced the Ku Klux Klan), worker's rights (The Bee has a strong history of supporting unionization), and environmental protection (leading numerous tree-planting campaigns and fighting against environmental destruction in the Sierra Nevada).