The 23-year-old England international had started brightly, creating chances and using his pace to trouble the City defence, but discomfort in his knee forced him off.
Arsenal manager Mikel Arteta confirmed the substitution was injury-related, saying: "He had an issue very early in the match and he wasn't well enough to continue." Arteta added that the move was precautionary, without providing further details.
Reports and fan concerns have suggested a possible anterior cruciate ligament (ACL) injury, which could sideline Madueke for a large portion of the season if confirmed.
However, some analysts note that no clear incident appeared to cause a typical ACL tear, raising the possibility that the scans may simply be precautionary.
The timing is particularly challenging for Arsenal, who are already managing squad depth issues in attack. Key forwards Kai Havertz and Gabriel Jesus are sidelined with injuries, leaving manager Arteta reliant on players such as Leandro Trossard, Gabriel Martinelli, Bukayo Saka, Eberechi Eze and Max Dowman.
Losing Madueke would be another significant blow early in the campaign.
Arsenal are next in action on Wednesday for their Carabao Cup third-round tie against Port Vale, followed by a Premier League visit to Newcastle United on Sunday.