The former Rochdale, Barnsley and Bolton Wanderers boss was appointed to the role at Prenton Park last November, steering them to a seventh-placed finish and a Papa John’s Trophy final appearance.
Assistant manager Ian Dawes will take charge against the Shrimps, aided by youth team boss and head of coaching Andy Parkinson.
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MATCH REPORT: Morecambe 1 Fleetwood 1
Explaining the decision, Rovers’ chairman Mark Palios said: “Despite success achieved on the pitch in the form of securing a place in the play-offs and reaching the Papa John’s Trophy final, in the play-offs an entire season gets distilled into two or three games.
“I have to do what I think gives us the best chance of achieving promotion in those games and I have reluctantly come to the conclusion that means making the change before the semi-finals begin.”
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