The foundation, which was founded in 2014 by the former world champion boxer Khan, has filed its accounts late in each of the past three years, with the paperwork for 2017 still outstanding.
In addition, the accounts do not break down how the foundation has spent its money, in breach of the commission’s rules on charities demonstrating their public benefit.
The 2015 and 2016 accounts show that the organisation spent just under £250,000 in two years on charitable activities, but there is no information about who received those funds. The accounts simply say the money went towards "relief of suffering".
"By reporting on public benefit, trustees identify that their charity is effectively doing what it was set up to do and is making a difference to its beneficiaries," the Charity Commission said in a statement about the case. "It is disappointing to see that this charity has not reported on public benefit.
"Separately, the public rightly expect charities to be transparent and accountable about the way in which they apply their income. A crucial factor in demonstrating transparency is meeting basic reporting requirements.
"The trustees of the Amir Khan Foundation have failed to submit their annual return and accounts on time for three consecutive years. This is unacceptable and we have reminded the trustees of their obligations."
The Amir Khan Foundation did not respond to requests for comment, but instead referred Third Sector to another charity, the Penny Appeal, which works to help people in 30 countries around the world affected by crises.
The Penny Appeal lists the Amir Khan Foundation as one of its partners in its own annual accounts. A spokesman confirmed that it received £50,000 from the foundation in the financial year 2015, and another £100,000 in 2016. This was followed by £147,765 in 2017 and £141,553 in 2018.