On 30 August 2016, Mustafi joined English club Arsenal for an undisclosed fee, reported to be in excess of £35 million. He made his debut in Arsenal's 2–1 Premier League win over Southampton at the Emirates Stadium on 10 September. Mustafi beat Bacary Sagna's record unbeaten start of 17 games at the club in Arsenal's 3–3 draw against Bournemouth with his 18th game without defeat. On 22 January 2017, he scored his first goal for the club in a home 2–1 league win over Burnley. Because of illness, he missed Arsenal's 2–1 win over Chelsea in the 2017 FA Cup Final on 27 May.