Under Clark, who is currently director and general manager, The Guardian went full colour before any other UK national title, as well as taking the brave move to a format never before used in this country.
Clark is moving as part of a shake-up at GNM that will also see marketing director Marc Sands leave the group.
He said: "I have thoroughly enjoyed my time at GNM and have been immensely proud to lead award-winning teams in advertising, newspaper sales and operations through some of the most challenging times and successful periods in this company’s history.
"Guardian News and Media is currently setting the agenda in the debate around how mainstream and new media co-exist."
Derek Gannon becomes director of operations and will take on responsibility for printing and distribution, while retaining the remit for technology, HR and other support functions.
Adam Freeman, currently commercial director of GNM, is promoted to director, consumer media. Colin Hughes joins the board in the new role of director of business and professional.
Jon Cornaby, who was appointed finance director in January, is also promoted to the board. Stella Beaumont takes up a new role, director, international and business development, focusing on the company’s growth outside the UK.
Tim Brooks, managing director of Guardian News and Media, said: "This new structure is designed to meet the longer-term needs of the business. Internally, it will allow swifter decision-making and better cross-platform working. Externally, we will be better equipped to meet the challenges of the rapidly changing media environment.
"On behalf of the entire company I would like to thank both Marc and Joe. They are popular, talented directors who have played an invaluable role in GNM’s success during their time here. Personally too, I would like to thank them for their contribution and support in the three years I have been MD. We all wish them the very best for the future."