The regulator announced on Friday that it had issued an order to direct the winding up of the charity, whose former patrons include Liam Fox, the Secretary of State for International Trade.
It said it had acted because of "various regulatory concerns about its management and administration, including that its assets may be at serious and significant risk of harm".
However, the findings of its inquiry have still not been published.
Afghan Heroes, which is based in Somerset, was founded in 2009 by Denise Harris, whose 26-year-old son Lee was killed while serving in Helmand Province that year. It offers care and support to veterans and their families,
The inquiry began in November 2013 after Afghan Heroes' accounts for the 2012/13 financial year showed it received £548,440 in 2012 but spent only £15,153 on charitable activities.
Fox stepped down the following month, citing a "breakdown in trust" with the charity. He said it had not informed him of the commission inquiry.
In February 2014 an interim manager, appointed by the commission, said the charity was "not viable and sustainable". It was subsequently prevented from fundraising or administering grants.
The commission has been criticised for the way it has dealt with the investigation and the length of time it is taking.
A Public Accounts Committee report in 2014 said the commission's handling of Afghan Heroes was evidence its "internal processes and investigations are slow and inefficient".
In November 2015 James Heappey, the Conservative MP for Wells, said people involved in the charity wanted to know what was going on and he had written to the commission expressing concerns that its "silence was rather deafening".
The commission said at the time its work was progressing "as swiftly as possible".
Its statement on Friday said its inquiry continued, adding: "A report setting out the findings of the investigation will be published once it has concluded."
Asked when that was likely to be, a commission spokeswoman said it would be in "due course".
The spokeswoman added: "We have endeavoured to progress this inquiry as swiftly as possible, but legal complexities have meant it has taken longer than we would have liked.
She said "limited assets" in the charity remained. "We are working to ensure these are dealt with appropriately as part of the final stages of the inquiry," she added.
Interested parties have 30 days to make representations about the winding-up order.
Heappey was unavailable for comment.