Yvonne Kucuk earlier this week said she would protect charities currently being forced out of the landord's premises by rent hikes and soaring repair bills.
The firebrand Eastender - a veteran community activist - did not specifically criticise City Property, which is wholly owned by the local authority.
However, she said: "No charity is going to be put out on my watch in my ward."
Labour insiders today insisted that her removal had nothing to do with her remarks about the underfire landlord firm, saying she had been removed from City Property's board to "lighten her workload".
The councillor today said she was unaware of the decision, adding: "This will mean I have more time to do my community work."
A spokesman for the ruling Labour Group said: "Councillor Kucuk had asked for a review of her council commitments, and in light of this, the Labour Group approved the appropriate changes.
"The details of these changes where clearly communicated to Councillor Kucuk prior to the Labour Group agreeing them."
Ms Kucuk is highly regarded in the party and is being widely discussed as a future Holyrood candidate.
Her remarks, published on Monday in the Evening Times, focused on her efforts to support City Property tenants, including charities, hit by rises in both rents and repair bills.
However, the councillor - along with Green Nina Baker and the SNP's Alison Thewliss - had championed their constituents affected by the problems on and around the Saltmarket.
Ms Kucuk plans to hold a meeting to bring together City Property and other agencies to help out affected businesses and charities, such as The Rooms, an Alcoholics Anonymous base facing closure after being told its rents would rise eightfold and it would have to pay £17,000 for improvements to its building on St Andrew's Street.
City Property, which is wholly owned by Glasgow City Council, was created to "buy" around 2000 business premises from the local authority in 2010.
The £120million raised funded a series of controversial early retirement deals.
However, City Property had to mortgage the property to pay the council - and now must raise rental income and cut costs to make loan payments.
Steve Inch, the council's former head of development and regeneration, is one of many critics.
He said: "The policy seems to have changed from 'securing good tenant mix' to 'securing full commercial rent'. That is not good regeneration."
David McDonald of the SNP praised Ms Kucuk's support for those affected by rising rents and repair bills
The councillor said: "I support the approach Councillor Kucuk is taking against the impact of these policies on charities across the city.
"So it is a real shame her voice will no longer be heard on the board of City Property."