The France international missed City’s trip to Brighton on Sunday, where the team fell 2-1 despite Erling Haaland giving them the lead.
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Cherki, who joined from Lyon over the summer, now faces a significant lay-off, with Guardiola confirming the extent of his absence.
“He’s out for two months. Seven or eight weeks,” Guardiola told club website.
January signing Abdukodir Khusanov made his first start of the season, and the manager was pleased with the Uzbek’s performance.
However, the defender was forced to leave the pitch with a knock just before the Seagulls secured all three points.