Interconnected Ventures, founded by Mbappe, has bought a majority stake in the French club through its investment arm, Coalition Capital.
France international Mbappe, 25, has reportedly invested around 15m euros (£12.6m) of his own money via the investment fund.
Coalition Capital replace previous majority shareholders, American investment fund Oaktree.
Pierre-Antoine Capton, current president of the club’s supervisory board, remains a minority shareholder.
“It is an incredible opportunity for Stade Malherbe Caen to be able to count on Coalition Capital for its development. Its values, commitments and extraordinary vision of sport are unique assets for this project,” Capton said.
Caen finished sixth last season and start their Ligue 2 campaign on 17 August against Paris FC. It will come a day before striker Mbappe could make his La Liga debut for Real Madrid against Real Mallorca after he moved on a free transfer from PSG this summer.
Caen were relegated from Ligue 1 in 2019.
A club statement said: “This transaction marks a significant step in the club’s strategic development and reinforces its natural ambition to remain among the historic places in French football.”