The commission said yesterday that it had opened a statutory inquiry into Afghan Heroes because of concerns about its management and low levels of charitable expenditure.
Fox, the Conservative MP for North Somerset, said in a statement that he had not been made aware of the inquiry by the charity, which he considered a "breakdown in trust", and therefore had decided to no longer act as its patron.
Afghan Heroes, a Somerset-based charity also known as True Heroes, was founded in 2009 to help existing and former military personnel and their families.
The charity’s latest accounts show that it had an income of £548,440 in the financial year ending 31 December 2012, but spent only £15,153 on charitable activities. A further £26,211 was spent on governance costs.
In 2012, Fox set up the initiative Give Us Time, which encourages members of the public to donate time in their holiday homes to military families, in partnership with Afghan Heroes.
In a statement, Fox said: "I have been made aware by media reports of the Charity Commission investigation into Afghan Heroes, of which I have been a patron.
"I hugely admire the principal ethos behind the charity, which aims to help service personnel damaged by deployment in combat. It is important to stress at this stage that this is an investigation and no conclusions about the running of the charity have been reached.
"However, I was not made aware by either the management or the trustees of the charity that any investigation was due to take place. With this breakdown in trust it is impossible for me to continue to act as patron and it is with great sadness that I can no longer do so."
No one from Afghan Hereos was available to comment on Fox’s decision to step down.
In September 2011, Atlantic Bridge, a charity founded by Fox to further public education on both sides of the Atlantic, was wound up by its trustees after a Charity Commission regulatory case report found that it promoted a policy closely associated with the Conservative Party and said that its "current activities must cease immediately".