Michael Clark was headhunted for the £50,000-a-year job to turn around the fortunes of the school. Yesterday it emerged he had left last week "by mutual consent".
The affair will embarrass the Conservative-led Wandsworth council, which has invested £2.2m in the scheme to turn a troubled comprehensive into a flagship institution.
Last March, the Office for Standards in Education (Ofsted) ruled that the college was failing its pupils. In response to the criticisms, new governors were appointed and an action plan of improvements approved by the then Secretary of State for Education, John Patten.
But a further blow came in the autumn when the college came fifth from the bottom of the Government's exam league tables.
Insiders said the fact that academic standards had not improved fast enough was influential in Mr Clark's departure.
Mr Clark was brought in as the former Battersea Park School was being relaunched as a showpiece college. His previous success in transforming an inner-city school in Newcastle made him an ideal candidate.
The college introduced a selective process - testing pupils for their aptitude in technology and a five-term academic year.
Despite the fact that the new college was over-subscribed, tension was mounting between the new regime and staff, who were asked to reapply for their jobs. Teachers complained of a lack of consultation and within six months many left.
Leaders of the local branch of the Nation Union of Teachers said they were not surprised that Mr Clark had now left. They insist there was too much emphasis on ideological theory imposed by the council and not enough on basics.
Yesterday a spokesman for the authority said a replacement would be chosen next week.