An investigation was launched into Winners' Chapel back in 2013 after claims were made that, amongst other things, large sums of money were being transferred to a sister organisation in Nigeria and conflicts of interest were leading to individuals benefiting financially from the church.
Clearing the church of wrongdoing, the Charity Commission said: "Our review of the charity's financial information identified minor discrepancies. However, the trustees were able to explain and resolve these.
"We found no evidence that £16 million or any other amount had been misappropriated. We were satisfied the charity could demonstrate good financial controls, appropriate for a large and expanding charity.
"We provided the trustees with general financial advice and guidance on best practice with regards to categorising expenditure, gift aid and grant making in their accounts."
The Commission has also ruled out any concerns over safeguarding and management of the church.
It said: "Our case, and this report, allows us to put on record that very serious concerns raised about a large charity were not substantiated.
"We provided the trustees with advice and guidance on preparing accounts to ensure that the minor discrepancies we identified are not repeated in future accounting cycles."
Winners' Chapel is a mega-church founded by Bishop David Oyedepo in 1981. Although the headquarters are in Nigeria, it has churches in 34 countries. Its London branch was the one investigated by the Charity Commission.