Mustafi, who moved to Switzerland as a child, began his career at FC Domat/Ems. In 2003, he was scouted by Grasshopper Club Zürich. After three years at Grasshopper Club Zürich, he signed for city and local rival FC Zürich in July 2006. He made just one appearance for Zürich, as a substitute against FC St. Gallen, and signed for FC Basel on a free transfer on 9 June 2008. His Basel debut came on 9 August 2008, in a 4–0 win over FC Vaduz at St. Jakob-Park, in which he got on the score-sheet twice. He made his first European appearance in a Basel shirt on 13 August 2008, as a substitute in a 0–0 draw against Vitória S.C. at Estádio D. Afonso Henriques in a Champions League Qualifying match. On 11 October 2009, FC Basel announced they had loaned Mustafi to FC Aarau until 30 June 2010. However, his time at Aarau was disastrous after Mustafi was among two other players to be omitted to the reserve side. After one season in Aarau, Mustafi returned to Basel only to be loaned out again, this time to German second division club Arminia Bielefeld. On 23 June 2011, Mustafi moved from Basel to Grasshopper Club Zürich, where he had played as a youth, signing a deal lasting until 2014. Ahead of the 2012–13 season, the club announced Mustafi will be joining a club on loan to gain first team place. On 1 August 2013, Mustafi signed for Scottish Premiership side Ross County on loan. Two days later at the start of 2013–14 season, Mustafi made his debut, coming on as a substitute in the 83rd minute for Kevin Luckassen, in a 2–1 loss against Celtic. Three weeks later, Mustafi scored his first goal in the second round of Scottish League Cup in a 3–2 loss against Stranraer. However, as the season progress, Mustafi struggled to earn the first team place, as injury progress. On 3 January 2014, Ross County announced that Mustafi had left the club following the end of his loan deal. Mustafi signed with Hong Kong side Kitchee on 29 November 2016 and was given the number 99 shirt. He made his debut five days later in a 0–0 draw against Eastern. On 11 January 2017, Kitchee terminated their contract with Mustafi. On 25 January 2019, Mustafi joined Young Fellows Juventus.
International career
Mustafi has represented Switzerland at under–19 and under–21 level.
Personal life
On 27 October 2008, he gained a Swiss passport, but also has Albanian and Macedonian dual-nationalities. Mustafi has declared to the media that he may play for Albania in the future.
