Stewart will work mainly with Pirates youngsters aged between 18 and 21.
The 39-year-old - who went on to represent Huddersfield, Ipswich and Sunderland at the height of his career - had been working in a coaching capacity at Exeter, where he hung up his boots in April 2011.
Stewart told Exeter's official website: "I've loved every minute of my time at the club both on and off the field. Having played and coached for three years it was great to be a part of the backroom staff.
"I wish Paul and the team all the best for the season. They'll be one of the first results I look for and I'm sure they'll have a good season."