The Scotland international was a big part of the Latics's FA Cup victory over Manchester City, but was unable to prevent the team from slipping down into the Championship.
Maloney, along with a host of other Wigan players, has been linked with a move away from the relegated club this summer, and the former Celtic man remains undecided.
|12/1||Wigan are 12/1 with bet365 to win the Championship next season
"Our chairman spoke about players leaving and staying, and us trying to bounce right back up.
"So there's a bit of uncertainty surrounding the club but when we come back for pre-season, and get a new manager named, things will be a lot clearer."
The 30-year-old played 36 league games for Wigan over the 2012-13 season, scoring six goals and assisting eight.