The strugglers succumbed 4-0 to the ruthless Robins on Saturday - and the Fleet manager has paid the price.
Assistant Anwar Uddin will also move on with senior player Josh Wright taking charge on Tuesday's home match with Aldershot.
The side sit bottom, claiming just a single point from their seven matches.
"Ebbsfleet United have today relieved first-team manager Danny Searle of his duties with immediate effect," a statement confirmed.
"The club would like to go on record as recognising the incredible job that Danny achieved last season in saving the club from relegation, after taking over initially as interim manager in February through to that memorable afternoon at Boreham Wood that maintained the Fleet’s National League status.
"It is with that very status in mind this season, however, that the decision has been made to part company with Danny after a start to the season which has fallen below expectations.
"Such a decision is never one that is taken lightly or without due consideration – but it must always be taken with the good of the football club in mind.
"The club would also like to thank Assistant Manager Anwar Uddin for his contribution to the club as he departs the Kuflink Stadium with Danny today.
"We wish Danny and Anwar every success in their future careers. Both men deserve all our gratitude not only for steering the club clear of relegation last season but for their immense hard work and dedication for the duration of their time at the club."
Searle said on Saturday that he knows results and performances must improve and fast but he refuses to call his players’ commitment into question.
He said: “To be honest, I’m a little lost for words. It’s hard at the moment, I would like to say sorry to the supporters who came up.
“When you’re in the position we find ourselves in, things sometimes just don’t go for you. We’re seeing that.
“There were spells where we looked good, but every time Altrincham came forward they looked capable of scoring against us and that’s a concern.
“I don’t think the players aren’t trying, they are, but we find ourselves in a difficult period and we need to get that first win as soon as we can.”