Now Khamenei has expanded Setad into a "financial juggernaut" that he has used to cement his 24-year grip on power, according to Reuters.
Under its orbit are 37 companies reaching into every corner of the Iranian economy - including finance, oil, telecommunications and even ostrich farming.
But the conservative ayatollah's transformation into an economic powerhouse also threatens to undermine his stated goal of presiding over a rapid rise in Iran's population, the investigation found.
In a glaring contradiction, ATI Pharmed, a pharmaceutical company run by Setad's charitable foundation, Barakat, embarked on a joint venture in May this year with a Swiss company, the Geneva-based Stragen Pharma, that included plans to produce oral contraceptives.
The initiative - in which the Iranian company has a 66 per cent share - jars with an edict issued by Ayatollah Khamenei to Iran's Health Ministry to scrap the country's liberal birth-control policy in an effort to raise the population - now about 75 million - to 200 million.
"The business empire controlled by Iran's Supreme Leader had grown so large that it now owned companies whose products Khamenei opposes," Reuters reported.
The economic encroachment has also had a baleful effect on workplaces. Employees at Parsian Bank, a private bank with more than 100 branches known for its liberal dress codes, experienced a culture shock when Setad's investment arm acquired a stake in the business in 2006. Male staff were banned from wearing ties while female employees received warning letters asking: "Why are you wearing jeans? Why are your lips red?"
The growth of Setad's business interests has attracted the attention of the United States Treasury, which imposed sanctions on the organisation and the companies under its wing last June as part of the international drive to pressure Iran to abandon its suspect nuclear programme.
The Treasury branded Setad - originally formed by the late Ayatollah Ruhollah Khomeini, the current supreme leader's predecessor - as "a massive network of front companies hiding assets on behalf of Iran's leadership".