The company, which is not replacing Baker directly, will divide her responsibilities among other members of management.
It has also hired its first senior marketer, Ed Aspel, who joins in the role of head of marketing from rival Yates, where he was sales director with board-level responsibility for marketing.
Baker joined JD Wetherspoon in 1992. She sat on the company's board and had overall control for food, distribution, marketing and commercial activities.
JD Wetherspoon's marketing has traditionally been focused on activity within its 650-strong pub portfolio, but Aspel's recruitment could see it embark on a wider communications strategy.
In the company's most recent results, for 2004-05, sales for the year increased by £22.7m to £809.9m, a rise of 3%, though pre-tax profits were down 15% to £46.1m.
The chain has being trying to cut costs across the business, both at head office and across its pubs.
JD Wetherspoon was one of the first national chains to pre-empt an expected ban on smoking in pubs. Chairman Tim Martin has been at the forefront of the campaign and has introduced a total embargo on smoking in 49 pubs nationwide.