The BBC reported that director of city development Dave Anderson said he wanted to pursue consultancy interests in economic development and investment.
An inquiry is currently under way into how building contracts were awarded for work relating to property maintenance.
Under the Edinburgh system, the council can intervene to organise repair work on private properties when the owners of shared buildings cannot reach agreement.
But hundreds of city residents complained they had been over charged for work while allegations of fraud and corruption have been investigated by police.
Eleven employees across the property service have been dismissed and six are suspended pending disciplinary action.
Anderson was suspended from his £123 000 a year job in June pending a disciplinary investigation into his management of the property conservation department.
He joined the council in 2008 from Scottish Enterprise.
An Edinburgh City Council spokesman told the BBC: said: “His decision to leave the council brings to a close the investigation into his knowledge and management of the issues under scrutiny in the council’s property conservation service.
“It can be confirmed that the investigation has not revealed any evidence to doubt Dave’s honesty, integrity and entrepreneurial abilities.
“We wish him well in his future endeavours.”