Boyata made his first Manchester City appearance in over two years when he started in a League Cup third round match versus Wigan Athletic on 24 September 2013. He helped his side keep a clean sheet in a 5–0 win, and came close to opening the scoring himself in the first half with a header that was tipped over the bar by the Wigan goalkeeper. On 4 January 2014, he was sent off for two bookings in the third round of the FA Cup, in a 1–1 draw at Blackburn Rovers. He was not included in City's matchday squad as they defeated Sunderland in the League Cup Final. Manchester City won the Premier League in 2013–14 but Boyata was not eligible for a medal as he made just one league appearance all season. On 28 May, Boyata signed a contract extension with Manchester City, which was due to keep him at the club until 2016.