The 30-year-old left-back has had a one-year extension automatically added to his existing contract after making 35 first-team appearances this season.
France-born Bakayogo, who has scored once in 57 games for the Alex, is now tied to Crewe until the summer of 2018.
He moved to Gresty Road in January 2016 after a two-year injury-enforced absence from the game.
Until being signed by then boss Steve Davis after an initial trial period, the ex-Millwall, Tranmere and Leicester defender had not played since rupturing his anterior cruciate ligament 37 minutes into his debut on loan at Yeovil from Leicester in January 2014.
Bakayogo, whose existing contract was to expire in June, was relegated to the bench following David Artell's appointment as manager in January, but the Ivory Coast international was recalled to the side because of Jon Guthrie's hernia injury.
Crewe defender Zoumana Bakayogo has earned himself a new extended deal after triggering a contract clause.