Saido Berahino's foundation failed to pass on funds raised at a 2015 event for WaterAid, the charity claims.
WaterAid says it "has not received any money" from a dinner the Stoke City striker hosted in Mayfair in May 2015.
The Charity Commission is "deciding if there are regulatory issues to assess".
The new agent of ex-West Brom striker Berahino declined to comment. However, BBC Sport understands the dealings with WaterAid were arranged by the 23-year-old's previous representatives.
"WaterAid was approached by the Saido Berahino Foundation in February 2015 regarding a dinner to raise funds for the foundation," a statement from the charity read.