The move is expected to be announced Tuesday.
Maloney, the assistant GM of the New York Rangers, takes the helm after Mike Barnett along with two other executives were fired in April when the Coyotes cleaned out their front office.
The Coyotes finished last in the Western Conference with a 31-46-5 record this season and missed the playoffs for the fourth straight season.
Maloney played 13 seasons in the NHL, including 10½ with the Rangers. After he retired in 1991, Mahoney joined the New York Islanders as an assistant general manager under Bill Torrey. He was promoted to GM two seasons later.
During his tenure, the Islanders drafted prospects Todd Bertuzzi, Bryan McCabe, Tommy Salo, Darius Kasparaitus, Scott Lachance and Zigmund Palffy.
The native of Lindsay, Ont., was hired by the San Jose Sharks in 1996, working as a scout before joining the Rangers' front office.
The Phoenix front office felt the fallout from the team's third consecutive last-place finish in the Pacific Division. Also dismissed were director of hockey operations Cliff Fletcher and assistant general manager Laurence Gilman.
Wayne Gretzky, who owns a share of the team and is its managing partner, will return for a third season as coach next fall.