On 28 August 2020, Elneny was in the starting 11 in the 2020 FA Community Shield, which Arsenal clinched a 5–4 victory over Liverpool in the penalty shootout after the match was 1–1 after 90 minutes. On 1 November 2020, Elneny put in an excellent display at the base of Arsenal's midfield alongside Thomas Partey to render Bruno Fernandes and Paul Pogba ineffective and earn Arsenal a first league win at Old Trafford since 2006. Elneny was praised by manager, Mikel Arteta after the game. While being away with Egypt during the International break in November 2020, it was confirmed by the Egyptian Football Association that Elneny tested positive for COVID-19 but showed no symptoms. After his return, he scored his first goal of the season in a 4–2 victory over Dundalk in the Europa League on 10 December 2020. His stunning strike outside the box was voted as the runner-up of the Goal of the Month on Arsenal's official website, also later on winning goal of the season. Elneny then scored another screamer versus Olympiacos on 11 March 2021, to keep Arsenal in the tie. On 2 May 2021, Elneny scored his first Premier League goal for Arsenal with a volley from the edge of the box in a game against Newcastle United.