The Nottingham Forest full-back, 21, joined the Iron at the end of January, but was forced to return to his parent club after suffering a season-ending knee injury in a challenge from the West Bromwich Albion winger Chris Brunt.
He had spent the first half of the season on loan at County, scoring one goal in 18 appearances for the side who went on the claim the League Two title.
Craig Short, who took over as County manager this summer, made Maloney one of his top transfer targets.
"He did well here last season until Christmas, I've spoken to Billy [Davies] about him coming here for the season and he's fine with it," he told the Nottingham Evening Post.