The regulator said in July that it had opened an operational compliance case on the charity after it bought a community radio station.
The charity, based in Haslingden, Lancashire, had also caused local controversy by attempting to sell a community centre given to it by another charity that had ceased operating. The sale did not go through.
According to its objects, Agapao International was set up to promote education and health, develop individuals and communities and to empower people.
The charity’s most recent set of accounts filed with the Charity Commission show that it had an income of £121,753 in the year to March 2012.
The commission said it had been working with the charity’s trustees to assess and resolve concerns about the governance of the charity.
A spokeswoman for the regulator said: "As part of our case, we instructed the trustees to carry out a review of the charity’s governance and activities. The trustees have informed us that, as a result of the review, they have decided to wind the charity up.
"In dissolving the charity, the trustees must follow due process, and we will be monitoring this to ensure that any outstanding charity assets are applied to appropriate purposes."
Nobody from the charity responded to requests for comment.