French midfielder Guendouzi, who is on loan at Hertha Berlin, will self isolate for 10 days.
The 21-year-old tested positive on two occasions on his return from international duty with France U21 and will now self-isolate for 10 days in Germany.
Guendouzi is reported to be asymptomatic and feeling well.
The Frenchman had no contact with any other Hertha Berlin players on his return, according to the club.
He was set to be presented to the media on Thursday afternoon and in line to make his debut in the Bundesliga fixture with Stuttgart on Saturday following his deadline day loan move from Arsenal.
Hertha Berlin said Guendouzi returned two positive tests on his return on Tuesday morningand Wednesday evening.
He had captained France U21 to victories over Liechtenstein and Slovakia in his first matches since last month’s international break.
The midfielder had been surplus to requirement at Arsenal since their 2-1 defeat to Brighton on June 20, where he was involved in a post-match altercation with Neal Maupay.