Although Bakes will still be at Crewe it is believed that he will still be in charge of the scouting system albeit on a part time basis.
56-year-old Baker joined Crewe in 1994 replacing Brian Eastwick as Dario Gradi's assistant manager.
Baker had a successful spell as manager at Leek Town where they reached the FA Trophy in 1990 and during the same year won promotion to the Unibond Premier League.
Earlier this week Baker was elected to the Leek Town board during the clubs AGM and had been working with Leek over the last few months as they managed to steer away from relegation under the guidance of former Crewe defender Neil Cox.