In 2004 the Foundation put a divide in the scientific and medical communities over the campaign to encourage general practioners to use and offer herbal and other various alternatives to treatments to National Health Service patients. Then in 2006 Charles made a speech to health ministers at the World Health Assembly in Geneva to urge them to develop a plan to add alternative medicine therapy to conventional medicine. In 2007 the foundation received a great deal of funding from the Prince’s Charities Foundation and an additional £300,000 grant from the Department of Health.

In 2010 there were accounting discrepancies noticed by the auditor and were reported to the Metropolitan Police and Specialist Crime Command. Two former officials were arrested for fraud that was believed to total £300,000.  Following the closing of the foundation many individuals and organizations launched a new organization called the College of Medicine, which was also supported by the Prince of Wales.