On 7 August 2015, Muniesa signed a new contract with Stoke keeping him at the club until the summer of 2019. He had his attempt saved by Simon Mignolet as Stoke lost in a penalty shootout to Liverpool, missing out on the 2016 Football League Cup Final. His 2015–16 season was disrupted by injury, playing in 17 matches as Stoke again finished in 9th position.