Having spent four years in the role at Portman Road, Clegg confirmed that the decision had been taken as part of a strategy to meet the financial challenges of the Financial Fair Play rules.
"As a result of the strategic review, it is clear that moving towards breakeven will challenge all clubs, not just Ipswich Town," he told the club's official website. "At the top of our agenda, and quite rightly, has been the priority to protect the playing budget.
"This, coupled with the owner's intention to play a more hands-on role has led me to the decision that now is the right time to seek a new challenge. Whilst we have been discussing this for some time, we agreed to leave any final decision until nearer the time when the rules are due to take effect, at the end of this season, and after the end of this last transfer window.
"I will be returning to my family in Surrey and over the coming months will be looking for my next professional challenge in international or domestic sport."
No replacement for Clegg will be named, with owner Marcus Evans thought to be taking on the role.