Dennis Wise has left his post as Millwall player-boss after a meeting with new club chairman Jeff Burnige.
Wise said he wanted to allow the new chairman a "fresh start"
"I've had a meeting with the new chairman, he told me his direction and I didn't agree," said Wise.
Wise led his team for the final time in a goalless draw with Burnley on Sunday as the Lions finished the season 10th.
Wise signed a new one-year contract in December but his future became unclear when chairman Theo Paphitis revealed he would quit at the end of the season.
Wise appeared alongside Paphitis after the game against Burnley to announce his decision.
"I have had a long chat with the players and have decided that as of now, I am stepping down as manager of Millwall," said Wise.
"I feel that it is important that the new chairman is allowed to get on with things; he has made it clear that he wants a fresh start and I think it is only fair that he is allowed to get on with it.
"I came in with Theo and I'm going with Theo. As far as (assistant boss) Ray Wilkins is concerned, he is meeting Jeff Burnige on Thursday, but he is totally separate to me."
Wilkins said earlier this season that he would not seek to replace Wise should he leave the club.
Wise grew increasingly frustrated during the season as he attempted to foster a potential working relationship with Burnige to match the one he enjoyed with Paphitis.
The former Chelsea and Wimbledon player described it as "difficult" in March and things grew frosty when he questioned the likely lack of investment under the new man.
"I want to stay. I have enjoyed myself here, I am ambitious," Wise said in April.
"I want to try to get the club out of this division. But you need help, and if you don't get much of that, it makes it very difficult."
Paphitis ploughed millions into the club during his tenure, but Burnige does not share his wealth and it had been widely reported that he wanted the manager to operate under tighter constraints and run a balanced budget.
Wise took the managerial reins at the New Den in October 2003, having joined the club as a player in September 2002.
In his first game in charge, Millwall beat Sheffield United 2-0 but Wise was sent off just four minutes after bringing himself on as a substitute.
The team reached the FA Cup final against the odds last season, losing 3-0 to Manchester United in the final but claiming a place in the Uefa Cup.
Paphitis said Wise's achievements were unlikely to be repeated.
"Dennis felt it was right to step down at this time," he said.
"It takes a very big bloke to put the club before himself, which is what Dennis is doing.
"He could have stayed, but Dennis feels it is right for Jeff and the club to move on.
"I would personally like to thank him for providing us with a couple of the most memorable years of our lives; years that are unlikely to ever be repeated."