The out-of-contract Frenchman has made over 200 appearances for the club after joining from Arsenal in 2011.
Clichy featured in the Premier League triumphs of 2012 and 2014 and also won the League Cup twice, in 2014 and 2016.
Earlier this week he stated he would not be staying at City and now the club have confirmed he will leave when his contract expires at the end of June.
"It's been a special six years for me at City," the 31-year-old told mancity.com.
"To win four major trophies and help establish the club as one of the top teams in English football has been an incredible journey that I'm proud to have been a part of.