The company said he would retire Jan. 1, 2011, and that Chief Operating Officer John Bryant would take over Mackay's position.
"This past summer, I became eligible to retire and made a commitment to spend more time with my famil," Mackay said in a statement. "I am pleased to pass the baton to John, whose management capabilities and wealth of experience have prepared him well to drive our business agenda for 2011 and beyond."
Bryant joined Kellogg in 1998 and has served as chief financial officer as well as chief operating officer.
Mackay, who will continue as a consultant through March 2011, has been with Kellogg 20 years, working as the CEO for the past four.