Emenalo's decision is a huge blow to Chelsea owner Roman Abramovich, who counted the 52-year-old among the few people he trusts and takes advice from.
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 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.
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The Sun has reported that Emenalo, who was the club's technical director for a decade, was considered a key ally of Conte's before he was informed that his services were no longer required.
'I wish Chelsea every success and look forward to following the club's future triumphs from afar'.
Chelsea chairman Bruce Buck praised Emenalo's work.
Head coach Antonio Conte's expressions of frustration at Chelsea's summer recruitment, plus some indifferent results, had led to speculation over his future but Conte and Emenalo had a good working relationship and the Italian said he was sorry to see him leave the club.
Emenalo was reportedly the man who earmarked Conte - who has been "rocked" by Emenalo quitting the club - as the manager to replace the sacked Jose Mourinho 18 months ago, and he had been in charge of the vast majority of Chelsea's transfer dealings over the past six years.