His arrival at the club, who drop down from the top flight to Premier 2 next season, follows the departure of Graeme Moffat, who is taking over as full-time director of rugby at Calgary Hornets in Canada. Moffat had been in charge at Inverleith for two seasons.
MacNaughton makes the move from Premier 2 side Peebles, where he has coached for the past five seasons. He has also coached at Currie and Murrayfield Wanderers. Peebles announced at the weekend Gary Parker will take over the reins next season. A statement from Stewart's-Melvlle said: "Bruce brings a wealth of experience to the club and he is looking forward to working with our young squad."