Cook guided Portsmouth to the League Two title in the 2016/17 season. Wigan Athletic On 31 May 2017, Cook was appointed manager of newly relegated League One club Wigan Athletic on a three-year contract, after a compensation package was agreed with Portsmouth. He led Wigan to the League One title and on an impressive FA Cup run that claimed three shocks against top flight opponents West Ham United, AFC Bournemouth and Manchester City. Cook resigned as Wigan manager on 29 July 2020, following the club's relegation from the Championship due to a 12-point deduction after the Latics entered administration. Ipswich Town On 2 March 2021, Cook was appointed manager of Ipswich Town on a contract until 2023. Cook's first match in charge was a 3–1 defeat away at Gillingham. His first victory as Ipswich manager came in his third game in charge, a 1–0 home win over Plymouth Argyle. On 7 April 2021, Ipswich Town was taken over by US investment group Gamechanger 20 Limited, with the club confirming that Cook would remain as manager under the new ownership. Ipswich finished 9th in League One at the end of the 2020/21 season. Ahead of the 2021/22 season, Cook oversaw a major turnover in both the playing squad and coaching staff, backed by the club's new US owners. Over a dozen first team players from the previous season departed with 19 new players joining. The players that departed included longtime club captain Luke Chambers, first team regulars such as Flynn Downes, Andre Dozzell, Gwion Edwards, Alan Judge, Emyr Huws and Teddy Bishop, and 2020/21 player of the season James Wilson. Despite these changes and many tipping the club for promotion, Ipswich made a poor start to the season, taking only two wins in their opening 10 matches. On 4 December 2021, with the team sat in 11th and 7 points adrift of the playoffs, Cook was sacked by the club. Having been in charge for just over 9 months, Cook is the second shortest serving manager in the club's history. Cook argued that he deserved more time in an interview a month after his dismissal, stating "If the new ownership had sat down and said to me at the start that if we didn't have instant success then [I would] be gone, then I wouldn't have stayed. That's my only regret." Return to Chesterfield On 10 February 2022, Cook was appointed