Downing, 38, played over 400 matches for Boro.
Boro academy manager Craig Liddle said: "It's nice to see former players come back as coaches.
"They know the club and they know what it's all about. They have a wealth of experience and knowledge, and it can only benefit the young players.
"Stewart himself has come up through the ranks of the academy, he had a great career, and we are happy to have him back."