The 52-year-old former Nigeria international has been one of Chelsea owner Roman Abramovich's key lieutenants, overseeing player and manager recruitment during a turbulent period during which he worked with 10 head coaches.
"This has been a very difficult decision to make, but one I believe is right for both myself and my family, and the club," Emenalo said in a statement.
British media reported that relations had been strained between Emenalo, director Marina Granovskaia and manager Antonio Conte, who made clear his unhappiness at the club's failure to sign top-level players in the last transfer window.
"It is with regret that the owner and board of directors accepted Michael’s resignation this week," Chelsea chairman
Bruce Buck said.
(Reporting by Neil Robinson, editing by Ed Osmond)
