Andy Hobsbawn, managing partner at Agency.com, will take over the running of the account, following Baker's decision to go on a sabbatical until the end of the year.
Baker said the break was part of Agency.com's sabbatical programme and that everything, "is amicable and agreeable".
He told Revolution: "It's the first opportunity I've had to take time off. I will definitely return. I don't have any other plans."
Baker moved to Agency.com four months ago from sister Omnicom shop Organic, where he was managing director.
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