The Telegraph reports the 53-year-old Emenalo has called time on his spell with the club after being appointed into the role in August 2011.
The former Nigerian worldwide, who was in the Super Eagles squad for the United States of America '94 World Cup, could assume a position at AS Monaco.
According to ESPN FC's Liam Twomey, it is unknown what impact his departure will have on the way Chelsea make decisions as a club and in the transfer market.
It is understood that Emenalo had become frustrated at being caught in the middle of a power struggle between Conte and the board.
Emenalo has been a driving force behind the club's policy to send a host of young starlets away from the club to further develop and Chelsea now have 34 players out on loan.
"'This has been a very hard decision to make, but one I believe is right for both myself and my family, and the club", he told the Chelsea's official website.
Emenalo's time at the club was never shy of controversy and reports of palpable discord between various individuals at respective times, but one can not deny that he played a major part in Chelsea FC's unprecedented success in the last 10 years. I wish Chelsea every success and look forward to following the club's future triumphs from afar'.
"Chelsea Football Club today announces that technical director Michael Emenalo has chose to stand down from his role", the club said in a statement.
It is believed that differences in the recruitment of players may have separated Emenalo and Conte, who he helped appoint in 2016.