Arguably owner Roman Abramovich's most trusted lieutenant, Emenalo has often been viewed as a controversial figure at the club.
In a statement on Chelsea's official website, Emenalo said: "This has been a very hard decision to make, but one I believe is right for both myself and my family, and the club".
The latest Premier League triumph came under current boss Conte in his first season in English football.
This news could have potentially huge repercussions at Stamford Bridge.
However Emenalo pointed to the success of Christensen, who impressed for Chelsea in their 1-0 victory over Manchester United at the weekend as proof that this system was working.
The 52-year-old has had a strained relationship with head coach Antonio Conte over the club's transfer business in the summer, and he's now quit the West London club to the surprise of many.
The former Nigerian global, who was in the Super Eagles squad for the US '94 World Cup, could assume a position at AS Monaco.
The Evening Standard claim The Blues are considering sharing out the former transfer guru's duties with director Marina Granovskaia and the scouting staff already in place.
Chelsea have been criticised in the past for their policy of signing up young and promising players before sending them out of loan for extended periods.