Baker, who co-founded Mozilla and helped create the Firefox browser, said she was stepping down to focus on her role as chair of the Mozilla Foundation, a nonprofit that promotes online freedom and innovation.
She said she was worried about the state of the web and the loss of public trust in technology. "We want to offer an alternative for people to have better products," she said, blasting the online giants that profit from spreading hate and misinformation. "What are the connections between this global malaise and how humans are engaging with each other and technology?"
Laura Chambers, a Mozilla board member and former Airbnb, PayPal, and eBay executive, will take over as interim CEO until a permanent replacement is found.
Chambers said she was keen to develop new products that protect users' privacy and challenge the dominance of the tech titans.
She said she joined Mozilla three years ago because she was "pretty disillusioned" by the impact of money and power on society. "I was confused about what to do and this felt like a genuine way to make an impact," she said.
Chambers said she was not interested in becoming the full-time CEO because she planned to move back to Australia for family reasons later this year.
She praised Baker for her leadership and vision, and said Mozilla was setting an example of how to manage a succession.
"I think this is an example of Mozilla doing the right role modelling in how to manage a succession," she said.