The former Aston Villa, Newcastle and Marseille defender returns to his old team barely a week after his sacking from fellow Ligue 1 club Rennes.
Beye started his coaching career as assistant manager at AS Poissy, ahead of a similar role with Red Star FC.
He took over a Stade Rennais at the beginning of 2025 and has left the club in six-place on the 2025/26 league standings.
He joins a Marseille side in fourth place as a replacement for Roberto De Zerbi, who left after 5-0 thrashing from Paris St-Germain and following their elimination from the Champions League.
A club statement read: "His deep attachment to Olympique de Marseille and his intimate knowledge of the environment in Marseille can be major assets in taking the club to the next step,"
Beye added: "I don't come to make up, I come because it’s my home."
Marseille are next in action away to 12th-placed Brest on Friday.