The City of London Police investigation comes just months after the Charity Commission criticised the "reckless" former trustees of the church for giving ex-Charlton defender Richard Rufus £5 million to undertake failed foreign exchange trades.
Rufus promised his then fellow trustees at the Kingsway International Christian Centre (KICC) an annual return of 55%, the commission said - but in reality the charity lost £3.9 million as a result.
The 41-year-old, who played more than 300 games for Charlton, was declared bankrupt in 2013 in the wake of investigations by financial authorities.
In 2015, a specialist civil court judge branded him a fraudster, saying he had "exploited trust and friendship" after running a Ponzi-like scheme which left investors millions of pounds out of pocket.
Rufus, a Christian, resigned as a trustee of the charity and the trustees who gave him the money between June 2009 and June 2010 without seeking independent advice first have also stood down.
Following the Charity Commission investigation, KICC's new trustees have agreed that their predecessors' decision to invest was "not a prudent or reasonable one".
The charity now has an investment manager and new guidelines.
A police statement said: "Detectives from City of London police's fraud teams are investigating.
"There have been no arrests."
KICC is famous for being one of the largest churches in the UK by congregation number, with thousands regularly attending on Sundays.