Mozilla co-founder Brendan Eich is stepping down as chief executive following protests over his support of a gay marriage ban in California.
The Mountain View, California-based non-profit maker of the Firefox browser infuriated many employees and users last week by promoting Mr Eich.
At issue was his $1,000 dollar donation in 2008 to the campaign to pass California’s Proposition 8, a constitutional amendment that outlawed same-sex marriages.
The ban was overturned when the US Supreme Court last year left in place a lower-court ruling striking down the ballot measure.
The contribution had drawn some negative attention in the past but took on more weight when he was named chief executive, and Mozilla employees and users criticised the move online.
Dating website OKCupid replaced its usual homepage for users logging in with Firefox, the world’s third-most-popular Web browser, with a note suggesting they should not use Mozilla’s software to access the site.
Mozilla chairwoman Mitchell Baker apologised for the company's actions in an open letter online, saying that Mr Eich is stepping down for the company's sake.
"We didn't act like you'd expect Mozilla to act. We didn't move fast enough to engage with people once the controversy started. We're sorry. We must do better," Ms Baker wrote.
She said that Mozilla believes both in equality and freedom of speech and that “figuring out how to stand for both at the same time can be hard”.
Mozilla is still discussing what is next for its leadership.
A representative for Mozilla could not be reached immediately for further comment.
Mozilla says about half a billion people around the world use Firefox, which has free, open software written in part by volunteers.
Google’s Chrome browser and Microsoft’s Internet Explorer are more widely used across desktops, tablets and phones.