It means he will essentially take the job of Flanagan, who had worked under Seibold during 2023 before joining the Dragons to relaunch his head coaching career.
The former dummy half, who also works in the media, will work specifically with the club in attack, and more specifically with the halves and hookers according to coach Anthony Seibold.
“Michael had a fantastic career as a player and is a premiership winner. He was a real leader at a couple of clubs he played at and also represented NSW," Seibold said in a statement.
“The thing I love about Michael since his retirement from playing is that he has worked for a couple of clubs in coaching positions.
“He has also done a lot of media, particularly around the X's and O's on rugby league, so he brings a lot of detail with what he does.
"Michael will be helping with our attack in 2024 and from a positions point of view, he will be working with our halves and our hookers.
“We feel as though he can help them improve individually but also us collectively from an attacking point of view, helping Steven Hales (Attack Coach) and also Mick Kulen (Football Analyst) in that space."
Manly are coming off a difficult first season under Seibold where the club finished in bottom half of the ladder, and will be desperate for improvement.
Ennis said he was excited to work with some of the game's best, and Luke Brooks.
“I'm also really looking forward to working with (new five-eighth) Luke Brooks. A change of scenery will be good for Luke. It will provide him an opportunity to play his best footy, which we saw at different stages of this year. He is a very good player when he is playing with confidence.
“One of the other players I am looking forward to working with is (hooker) Lachlan Croker. I have just admired him from afar with his work ethic and his toughness. I feel there are areas of his game that I can help him with.
“I've been highly impressed with ‘Seibs' in the early conversations with him and his staff. There is a great coaching staff there and I'm very happy to be joining them and sharing some of my experiences in the game.”
It's unclear whether Ennis will continue working with Fox Sports as part of his new role, although Flanagan was able to work as a commentator throughout 2023 while part of Manly's coaching staff.