Emenalo, one of owner Roman Abramovich's most trusted advisors, joined Chelsea 10 years ago and was crucial to the club's scouting success during that time.
Emenalo said it had been a hard decision to make, adding: "I have had the privilege to work alongside some of the most talented people in the world of sport over the past 10 years and I will depart incredibly proud of the achievements we have made. I have had the privilege to work alongside some of the most talented people in the world of sport over the past 10 years, and I will depart incredibly proud of the achievements we have made".
Conte won his first title with the Blues in his debut season, the club's second league title in three years.
This news could have potentially huge repercussions at Stamford Bridge.
Further, the resignation is thought to be due to differences with influential director Marina Granovskaia over Antonio Conte and several key transfer decisions, and the general direction in which the club was headed.
Michael Emenalo has shocked Chelsea by deciding to step down from his position as technical director.
The former Nigerian footballer has done well to recruit some big names since joining in 2007, helping Chelsea to eight trophies.
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.