Baker has now been employed by the Prince of Wales as a consultant on a range of other projects.
Waitrose signed a licensing agreement in September that will allow it to expand the Duchy range, which was founded by the Prince in 1990 to support British farming and raise money for charity.
Baker has been working from an office at Clarence House since the deal was completed, shortly after which Duchy's office in Richmond closed.
A spokesman for Baker said that he was now "involved in a whole series of projects relating to Clarence House and the Prince of Wales' interests", including promoting the Highgrove shop and food range, which is now stocked in Ocado, and as a non-executive director of Mey Selections.
"He still retains a role working with Clarence House but it is changing to reflect some of the other interests of His Royal Highness," said the spokesman. "The day-to-day marketing of Duchy is already part of Waitrose."
Last month, Baker told The Grocer that he was still "very much the chief executive of Duchy Originals".
However, the spokesman said Baker would retain a role at Duchy "only in the very, very broadest sense".
"He is one of the people at Clarence House who at the very highest level, almost a philosophical level, has a view on the brand," he added.