The Christ Embassy church denomination, founded by Pastor Chris Oyakhilome has oversight for 90 churches across the country.
An inquiry was opened into the charity, following a number of concerns about the use of charitable funds on large connected party payments.
The Charity Commission's investigation found a number of informal grants and payments had been made to affiliated organisations.
Between 2009 - 2011, the charity gave over £1.2 million to a broadcasting company, Loveworld Television Ministry, which was wholly owned by a trustee of the charity.
Loveworld was also given use of a £1.8 million property purchased by the charity, free of charge for six years.
It is not unlawful to make positive collaborations to linked companies, according to the regulator, so long as they are appropriately managed.
The inquiry found a lack of formal contracts or appropriate record keeping, and a lack of evidence of conflicts of interest being appropriately managed as well as poor financial management.
Two members of the charity's board of trustees resigned after the regulator took action to have them removed upon concluding serious misconduct and/or mismanagement had taken place.
The Commission also took temporary and protective action by freezing bank accounts, to protect over £600,000 of charitable funds, and appointing an interim manager who took over the running of the charity to the exclusion of the trustees, after identifying issues of unauthorised use of charity premises as a place of worship, and significant penalties incurred due to late tax return submissions.
The interim manager instigated a full governance review, following which a new board is making significant progress to address the issues and improve oversight and control of the charity.
Amy Spiller, Head of Investigations Team at the Charity Commission said: "This was a complex inquiry that unveiled numerous failings by those running Christ Embassy over a number of years, which exposed the charity to undue risk. I am pleased that these issues have been resolved and that the new board of trustees has shown a clear commitment to move the charity forward responsibly.
"Those running a charity should always be guided by their charitable purpose. Trustees have an important responsibility to ensure that they act in the best interests of their charity at all times, and take care to safeguard their charity's assets. Our guidance around governance arrangements is there to help trustees ensure they do just that.
"Charities are trusted in a way that is unique, and people often put a lot of faith in religious charities. It is therefore vital that trustees, particularly those with a large following, do all that they can to inspire public trust, so that they can help to uphold wider public confidence in charities."
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