Joly, who was the beverage director at the experimental cocktail bar, is said to want to explore other opportunities when he departs later this month.
Micah Melton, who's been with the bar since its inception, will take the reins at the bar that was voted 13th best in the world.
As Diageo’s current World Class winner, Joly will have the opportunity to travel the world as an ambassador for the competition.
A statement on the bar’s Facebook page read: “Our friend and co-worker Charles Joly will be stepping down as the beverage director of The Aviary at the end of this month.
"Almost three years ago we sat down with Charles and discussed what would happen if we took a great classical bartender and inserted him in The Aviary's environment of no-rules innovation. It felt like a risk for both parties which meant it was a great idea.
"The results have been terrific. We've all learned a great deal and most importantly our patrons have enjoyed the dynamic and delicious drinks.
"It's not surprising given his professional and personal success that Charles has decided to pursue the unique opportunities which his current status as Diageo World Class winner present: travel, consulting, continuing education and entrepreneurship.
"We wish him every success and know that he will continue to be a great ambassador for cocktails in America and beyond... and a classy representative of The Aviary and the city of Chicago.
"Micah Melton has been promoted to Beverage Director of the Aviary. Micah has been at The Aviary since we opened and has been understudy to Charles for over a year. He has also been the driving force of our beer collaborations, many of our specialty drinks, and day to day management of operations. To say that Micah has earned the position is a vast understatement. He lives and breathes the Aviary and we're grateful for his leadership.”