Boyata made his first team debut against Middlesbrough in the FA Cup third round on 2 January 2010, playing centre-back and helping his side to a 1–0 win at the Riverside Stadium. His league debut was as a substitute against Blackburn Rovers nine days later, replacing Martin Petrov in the 86th minute of a 4–1 home win. His first start in the Premier League came away against Hull City on 6 February. He was named young player of the 2009–10 season for his efforts during both legs of the League Cup semi-final against rivals Manchester United.
Belgium manager Georges Leekens selected Boyata for two Euro 2012 qualifiers against Kazakhstan and Austria in late 2010. He didn't play against Kazakhstan, but made his debut against Austria on 10 October 2010, coming on as a half time substitute for Toby Alderweireld in a 4–4 draw. He received a call up for a friendly match against Slovenia in August 2011, but did not play.