Born in Uccle, Belgium, Boyata started his career in the youth team at Brussels before joining Manchester City in 2006. He was part of City’s 2008 FA Youth Cup winning side, starting in both legs of the final against Chelsea. He won City’s Academy Player of the Month award for April 2009. He was one of seven Academy players from his year to be promoted to training with the senior players from the start of the 2009–10 season.

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.

On 26 August 2011, Boyata joined Bolton Wanderers on a season-long loan. He made his starting-eleven debut for Bolton Wanderers on 10 September playing the full game of Bolton’s 5–0 home defeat to Manchester United. On the 2 October 2011, Boyata scored his first goal for Bolton Wanderers in 5-1 away defeat against Chelsea. Boyata sustained an ankle injury in the 2–0 loss to Sunderland on 22 October and the injury, which kept him out for six weeks, meant that Boyata, as part of his loan agreement, returned to Manchester City for treatment. He returned to the Bolton starting line up in the match at Tottenham Hotspur on 3 December.

On 31 August 2012, Boyata left Manchester City to join Dutch Eredivisie club FC Twente on a short-term loan. He made 8 appearances for FC Twente before rejoining Manchester City on 8 January 2013.

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.

On 10 August, Boyata played the full 90 minutes as City opened the season with a 3–0 defeat to Arsenal in the 2014 FA Community Shield. In all, he made six appearances in his final season, with one start from two in the league.

Boyata signed for Scottish Premiership champions Celtic on a four-year contract on 2 June 2015, for a fee of about £1.5 million.

He was recalled to the Belgium squad in October 2015 for Euro 2016 qualifiers against Andorra and Israel. He didn’t play in either of these games, but was called up again for a friendly against Portugal on 29 March 2016. He won his second cap in that game when he came on as a substitute after 86 minutes for Jason Denayer.

Boyata found himself out of the team at the start of season 2016–17, but worked hard in the gym to improve his fitness. His first start (and appearance) of season came in the 1–0 Scottish Premiership victory at Kilmarnock on 18 November 2016. Boyata did not make his second appearance of the season until the 3–0 Scottish Cup victory at Albion Rovers on 22 January 2017. He scored two goals in his next three league appearances at Celtic Park, both headers from set-pieces, in 1–0 wins against St Johnstone and Aberdeen respectively. Boyata re-established himself in the team, having followed advice from manager Brendan Rodgers: “He [Rodgers] wanted me just to play simple and to play as I did in training and he said that everything would go well if I did whatever he told me.”

In May 2018 he was named in Belgium’s preliminary squad for the 2018 World Cup in Russia. On 4 June 2018, Boyata was named in the final 23-man squad for Belgium at the 2018 World Cup. He played every minute of Belgium’s group stage games at the 2018 World Cup, however he was dropped for the rest of Belgium’s games in the knockout stage as Belgium finished third.

In May 2019, Boyata joined Hertha BSC on a free transfer. Boyata scored his first goal for his new club on 29 September 2019, completing the scoring in a 4–0 victory over 1. FC Köln.