The left-back, 27, faces four counts of rape and one of sexual assault after being arrested at his £5m home, police confirmed.
He was immediately suspended by the club pending an investigation.
Detectives said the charges relate to three complainants — all over the age of 16 — and are alleged to have taken place between October last year and this month.
The French international was arrested last November at his £5million home in Prestbury, Cheshire.
“The matter is subject to a legal process and the club is, therefore, unable to make further comment until that process is complete.”
Cheshire Police said the Crown Prosecution Service authorised the charges to be brought.
Premier League champions Man City spent a reported £49.2million signing Mendy from French side Monaco in 2017.
But he was part of the squad that defeated Norwich 5-0 last weekend.
In September last year City boss Pep Guardiola revealed Mendy would be out of the game for at least a month due to an injury.