Skuse captained the side on the opening day of his first campaign in League One in 12 seasons, with regular captain Luke Chambers out through suspension. Skuse started the club's opening 17 games of the season in the league, mostly alongside Flynn Downes in midfield. After captaining the side in a goalless draw against Gillingham, which saw Ipswich go winless in six matches and drop out of first place around the turn of the year, Skuse was dropped from the side by manager Lambert and replaced by Emyr Huws. He made his first start in seven matches against Peterborough on 1 February. At the time of the suspension of the season due to the COVID-19 pandemic in England, Ipswich were on a run of four defeats and had fallen to 10th in the table. Skuse had made 25 starts and four substitute appearances in the league. He captained the side in both matches in the EFL Trophy after the group stage, which ended for Ipswich in Round 3 against Exeter. He also captained the side in the club's final match in the FA Cup that season, against Coventry in a second round replay, his only appearances in cup football that season.