As part of the documentary Landlords from Hell, which was broadcast on 4 July, an undercover reporter was sent to work for the charity.
The programme alleged that the organisation, which lists among its charitable activities "the provision of housing with no deposits and discounted rents", was charging deposits and had evicted tenants in order to bring in new tenants at higher rents.
In the programme, the presenter Jon Snow said some of the charity’s properties had been left in a state that was "completely beyond habitation" and that it had mistreated tenants. "It seems extraordinary that they are a charity," he said.
Bill Rashleigh, the media officer with responsibility for investigations at the housing charity Shelter, said on the programme: "I find it hard to believe that the Charity Commission has it registered.
"I’m not sure what its charitable objects are, but I severely doubt it’s fulfilling them."
Speaking to Third Sector today about the commission’s decision to launch a formal inquiry, Rashleigh said: "It’s about time. Some of the practices at this charity were beyond belief."
In the programme, the undercover reporter asked a member of staff at the charity what the difference was between the foundation and the private firm Meridian Investments. She responded: "It’s the same company."
A spokeswoman for the Charity Commission confirmed it had received 25 complaints about the charity after the programme was broadcast.
In a statement, she said: "Concerns have been raised regarding the treatment of beneficiaries of the charity, including some classed as vulnerable beneficiaries.
"As part of our investigation, we will consider the risks to the charity’s beneficiaries, its financial controls and management, any conflicts of interest and whether there has been any mismanagement or misconduct on the part of the trustees.
"We will also consider the Meridian Foundation’s role and relationship with non-charitable organisations including Meridian Investments (Manchester)."
The statement said the commission could not investigate issues relating to the quality of accommodation, which was the responsibility of the local authority and other regulators.
The charity’s most recent accounts, which cover the year ended January 2010, show its income in that year was £173,437.
The Meridian Foundation did not respond to repeated requests for comment.