Bethel United Church of Jesus Christ Apostolic UK came under question after a late submission of its annual records.
The Commission says it's worked with leaders to ensure £1.2 million is now accounted for.
Opening an inquiry in March 2017, it found the former trustees responsible for misconduct and mismanagement in the administration of the charity. This included a failure to manage the charity's funds appropriately.
A new board of trustees has now been brought in.
Harvey Grenville, Head of Investigations at the Charity Commission said: "It is unacceptable that this charity has repeatedly found itself subject to regulatory scrutiny.
"The former trustees failed to meet the expectations of the public and the charity's beneficiaries in terms of transparency, accountability and the careful stewardship of charitable funds.
"I expect the new board of trustees to continue making good progress, thereby returning the charity to a sounder footing.
"The public deserve to be able to understand how their donations are being spent, and see clearly that they go towards their intended causes. As a result of our inquiry significant charitable funds are now accounted for."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.