Transport for London said that the cheese element of Cheesegeek’s billboards did not comply with their advertising standards.
TfL uses the Food Standards Agency’s model to define foods that are high in fat, sugar and salt.
Cheesegeek founder Edward Hancock found success on Dragons’ Den last year.
He secured a £150,000 investment from Dragon, Steven Bartlett, for a 5% share in the business.
The cheesemonger, which is based at the industrial units in Station Approach, has called the policy “extremely simplistic”.