Graham Hilton was suspended from Halton college at the end of October, just as it was about to be inspected by the Office for Standards in Education.
He had been attempting to restructure the college. Ray Dowd, who is temporarily acting as part-time principal, has denied that this had anything to do with his departure.
Mr Dowd is principal of nearby Wirral Metropolitan college.
Mr Hilton had been in post for less than a year.
A college statement said Mr Hilton had decided to resign and his "considerable contribution" to the college was praised.
Mr Hilton was seen as a rising star by ministers for his implementation of the Government's "Success for All" further education strategy.
He was brought in to advise ministers, using his own college as a case study, after a few months in the job.
Halton ran into controversy over uncontrolled franchising of courses in the late 1990s.
Peter Kent, the chairman of governors, has refused to comment.