The National League club have made the decision not to extend the contract of Kevin Watson, which elapses at the end of the month.
The 46-year-old was appointed in November, taking over from Garry Hill.
He put the club back in with a chance of survival and Fleet were just a point away from exiting the drop zone when the season came to an early end.
The club have thanked Watson, the former Rotherham and Reading midfielder, for his seven months in charge.
A statement read: “The club would like to place on record its thanks to Kevin and his staff for their efforts to stabilise the season, achieving 17 points from nine matches leading into the lockdown and eventual cancellation of the season.
“Kevin was appointed to the role under difficult circumstances and after a poor start to the season. The club would like to thank him for stepping in and stabilising results in the New Year prior to the premature end to the season the global coronavirus pandemic necessitated.
“The club wishes Kevin all the best in the future and are grateful for his efforts during his tenure here at Ebbsfleet United FC.”
Going forward, the Kent club confirmed: “Director of football Steve Lovell continues to oversee recruitment and retention. The club will provide an update on the future football performance structure in due course.”