Peters' decision comes after an eventful week on the South Coast, which saw the Exeter City Supporters Trust taking control of the club yesterday following the departure of John Russell and vice-chairman Mike Lewis.
Peters only took charge of the Grecians in February, but despite a late fightback Exeter were relegated to the Nationwide Conference on the last day of the season.
Steve Perryman has been asked to take over team affairs in a temporary advisory role.