Clegg has been with the Robins since November 2019, having joined the club from Atherton Collieries, where he won three promotions during his five years in charge.
It has been a difficult festive period for the club, with 4-0 and 6-0 defeats to local rivals FC United of Manchester and Hyde United leaving them 12th in the Northern Premier League table.
The Robins have lost four of their last six league fixtures, winning just once.
Confirming Clegg’s departure, a club statement read: “Recent results have not been up to the high standard that both Michael and the club would expect, with both parties accepting that the time has now come for a change in direction."
Joint chairmen David Burke and Jonathan Sayer said: "We have the utmost respect for Michael, and the work he has put into Ashton United has been immeasurable.
“Sadly, that effort has not brought the successful outcomes on the pitch that we all desire. Everyone at the club wishes Michael and his management team well for the future."
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