The commission began probing the charity shortly after David Philpott, its chief executive, was dismissed after only 12 weeks in the job.
Philpott had been investigating allegations of malpractice at the charity, which is also called Virgin Hems London, when he was escorted off the premises by trustees in November last year.
A commission spokeswoman said: "Concerns were raised with us about governance and financial controls at Virgin Hems London. Having considered the concerns raised, we have given advice and guidance to the charity on a number of issues. Provided the trustees implement our recommendations, there is no further role for us in this matter.
"We also received complaints about an employment matter at the charity. The commission cannot generally become involved in employment issues in charities as these are a matter for the charity trustees to decide. We therefore did not consider the employment issues raised with us during our case, and we advised the complainants of this."
The spokeswoman said she was unable to go into detail about the nature of the advice.
London's Air Ambulance refused to elaborate other than to say the advice and guidance involved procedures and would be implemented immediately.
Dr Gareth Davies, the charity's chair, said: "We are delighted that the commission has been so supportive and given the charity a clean bill of health."
Philpott was unavailable for comment.