Michael Jackaman, chairman of the international food retailing and drinks group, said the changes were an "evolutionary step" in a more focused business.
Mr Macfarlane becomes chairman of the Lyons food manufacturing businesses, which are up for sale, and vice-chairman of the Domecq drinks company bought for £719m last May. "It is a sideways move in the sense that it is not up, or down. But it is an important job," Mr Jackaman said.
He added: "He's not the world's best presenter, and there have been mumbles from time to time from analysts. But the accusation about being sidelined is completely unfounded ... Peter emerged clearly as the right person for Domecq."
Tony Trigg, chief executive of the group's retailing side, becomes finance director. Tony Hales, chief executive, is now also deputy chairman of the Carlsberg-Tetley joint brewing venture, following the retirement of Roy Moss. Stephen Alexander, currently managing director of Lyons, succeeds Mr Trigg at Allied Domecq Retailing.