As a result they will all own an equal share in the club and have a vote on transfers, player selection and all major decisions.
They will also have an option to buy all the club for a fixed price in future.
As part of the deal, the current board will continue their roles at the club as non-executives.
The club staff, including manager Liam Daish, are expected to stay on. Daish, whose title will become head coach after the takeover, said: "As a football fan, I think the idea is fantastic.
"I look forward to the challenge of working with thousands of members to produce a winning team. Alan Kimble [assistant] and myself are 100% committed to making this work."
Chairman Jason Botley said: "The board, the coaching staff, club employees and myself are united in believing this is a great opportunity for Ebbsfleet United.
"This extra finance and support will enable our club to progress."
MyFootballClub's Will Brooks said: "Nine football clubs approached us and we believe that Ebbsfleet is the right choice.
"We hope that MyFootballClub members and Ebbsfleet supporters will join forces to make the football club more sustainable and successful."