The defender had surgery on his left knee in Barcelona after pulling out of the France squad, City confirmed.
It is a meniscus problem and not a repeat of the cruciate knee ligament injury which saw him miss the majority of last season.
No time frame has been given for the full-back's recovery.
"Surgery was conducted on Wednesday evening and everyone at Manchester City wishes Benjamin a speedy recovery," a City statement added.
Mendy played 90 minutes in City's 3-1 Manchester derby win on Sunday but withdrew from international duty afterwards.
The 24-year-old was assessed by City's surgeon Dr Ramon Cugat in Barcelona before having surgery.
Mendy, who has nine caps for France, suffered a cruciate knee ligament injury in September 2017 before returning in April.
He made seven appearances in City's title winning season last term, enough to earn a winners' medal having joined from Monaco for a reported £52million.
Fabian Delph, Danilo and Oleksandr Zinchenko are options to replace him at left-back for City boss Pep Guardiola.
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies