His departure comes a little less than two years after he publicly accused his boss, Mark Shuttleworth, of making sexist remarks in a keynote speech at a conference.
Zimmerman is apparently looking for "new challenges" and to "stretch myself in new ways" after joining Canonical as part of the team that started the Ubuntu GNU/Linux distribution in 2004.
He intends to remain on the technical board of Ubuntu. Recently he rejoined Debian as a fulltime developer and intends to continue in that role as well.
Zimmerman has also been in involved in the Ada Initiative (which aims to increase the participation of women in free and open source software), and the FreedomBox Foundation (that intends to provide free software to run on a personal server aimed at preserving privacy) in an advisory role and intends to continue with those organisations as well.
"I'll be moving back to the US, closer to old friends and family, and starting a new job with a different type of company," Zimmerman wrote on his personal blog.
"I am leaving behind a capable and dedicated team at Canonical, who I am confident will achieve even greater things in the years to come."
Last month, Ubuntu released version 11.04, a release that incorporates new technologies like the Unity desktop and the Wayland server.