Trotter played 12 times on loan at Glanford Park during the 2009/10 season, scoring once.
Nigel Adkins, the Scunthorpe manager, offered the midfielder a contract last summer but he opted to stay with Ipswich.
He signed a one-year contract with the Tractor Boys after being told by their boss Roy Keane that he was seen as a first-team player, but struggled to break into the team.
He spent the latter part of last season with the Lions, helping them win promotion to the Championship via the League One play-offs.