Pert quit on Thursday and will depart his post at the end of the year, though he is set to stay on as a consultant for Melbourne's bid to build a new training and administration base at Caulfield.
Ex-Collingwood CEO Pert, who joined Melbourne at the end of 2018, follows former president Kate Roffey who stepped down in September amid an ongoing period of turbulence.
Demons star Christian Petracca addressed the club's culture on Thursday. (Joel Carrett/AAP PHOTOS)
Pert's departure comes ahead of a likely board reshuffle as the Demons prepare to hand down findings from two separate reviews into their operations.
The news was announced via a letter to members from president Brad Green, who hailed Pert's "invaluable contributions" and leadership.
"It is with mixed emotions that I announce that, after six years as CEO of the Melbourne Football Club, Gary Pert has decided to retire and will step down from his role," Green said.
"After careful consideration of what is best for the club, his family, and his own future, Gary concluded that now is the right time to initiate the search for his successor.
"I want to make it absolutely clear that this decision, including its timing, is Gary's own."
Melbourne have been wracked by turmoil almost since their breakthrough 2021 premiership.
They suffered straight-sets finals exits in 2022 and 2023 before missing the top eight altogether this year and finishing 14th.
Queries over their off-field culture have popped up consistently, and weren't quashed by Pert's extraordinary claim late last year that the club's culture was the best he had seen in 40 years.
Clayton Oliver's off-field troubles, Joel Smith's anti-doping case and disgruntled star midfielder Petracca's desire to leave the club following his horror injury in the King's Birthday match, were headline issues.
Petracca ultimately committed to the Demons, for 2025 at least, on August 31, while Melbourne shut down any chance of Oliver moving to Geelong after Pert had reportedly shopped him around.
Speaking to media on Thursday, for the first time since his trade saga, Petracca was asked if he was happy with the culture at Melbourne.
"I think so. Culture is an interesting word. It's a high-performance industry and for me we're always trying to improve and get better," Petracca told reporters at a Melbourne Cup promotional event on Thursday.
"For me, getting people through the door is the right thing.
"We've had healthy conversations and that's awesome. Like any industry and any club, we're looking to improve."
Green is reviewing the club's board while Melbourne have enlisted former All Blacks manager Darren Shand to look at their football department.
Former Melbourne footballer, lawyer and ex-Melbourne Cricket Club president Steven Smith will stand for board election, along with businessman Chris Barlow.
"Should members elect him, I will encourage Steven to seek board endorsement to succeed me as president of the Melbourne Football Club at the end of the 2025 AFL season," Green said.
Chief operating officer David Chippindall will serve as interim CEO from January.
