Jurors could not reach verdicts on one count of rape and one of attempted rape, following a six-month trial.
Mr Mendy and his friend Louis Saha Matturie, 41, were accused of various sex offences against young women.
Mr Matturie was also found not guilty of three counts of rape at Chester Crown Court.
Jurors failed to reach verdicts on three counts of rape and three counts of sexual assault against him.
Mr Mendy covered his face with both hands as the jury foreman repeated “not guilty” to the six counts, which related to four young women or teenagers.
The unanimous verdicts were delivered on Wednesday by the seven men and four women on the jury, one juror having been discharged earlier for medical reasons.
The verdicts could not be reported until jurors concluded considering the remaining two counts, after they were given a majority direction by Judge Steven Everett, meaning he would accept a 10-1 majority on any verdict.
Mendy, of Mottram St Andrew, Cheshire, had denied all charges. He has been suspended without pay by Manchester City since first being charged in September of 2021.
After the jury was discharged Matthew Conway, representing the prosecution, said that they would be seeking a retrial on the two counts the jury could not reach verdicts on.
In a statement, Man City said: “Manchester City FC notes the verdict from Chester Crown Court today, where a jury has found Benjamin Mendy not guilty of seven charges. The jury is hung on two charges and the trial is now over.
“Given there are open matters related to this case, the Club is not in a position to comment further at this time.”
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