Skuse was partnered with Brentford signing Jonathan Douglas during the 2015–16 season. On 19 October, Skuse signed a new contract, keeping him at Ipswich until 2018 with a year's option. He made his 100th appearance with the club two-week's later against Cardiff. After a draw against Wolverhampton on 21 November, manager McCarthy spoke of Skuse as a "Premier League footballer". Skuse made 39 starts in the league that season, missing a month after sustaining a toe injury on 6 February against QPR. He wore the captain's armband from the start for the first time on 30 April, in a win over MK Dons. Ipswich finished the season in 7th, five points off the promotion play-offs.