The United Hands Foundation Australia has run the Engine Room Cafe in Teneriffe since 2016, moving into the historic 1920s-era building after council restored it.

A council spokeswoman said the business had "failed to meet the requirements of their lease agreement with council".

UHFA was contacted for comment.

"The agreement with the Engine Room operator remains in rental arrears, despite council offering payment plans, business coaching and mentoring," the spokeswoman said.

"Council is now in the process of securing a temporary operator, before a more permanent operator is secured through a competitive tender process."

Council infrastructure chairman Amanda Cooper said the operators had been told "enough is enough" after issues had emerged.

“Council is committed to delivering value for ratepayers’ money and the information provided when selecting the operator indicated this would provide the best outcome for the community," Cr Cooper said.

“Unfortunately, issues began to emerge and the operators have been told enough is enough after consistently failing to meet their obligations to both the community and their lease agreement."

In 2016, Brisbane lord mayor Graham Quirk announced the planned cafe in the old engine room would be run by a charity, with social enterprise charity UHFA one of two bidders.

UHFA bid a base rent of $35,000 per annum, plus percentage rent of 2 per cent of sales over $800,000, 3 per cent of sales over $1 million and 5 per cent of sales over $1.5 million.

The cafe ran into some controversy in 2016 after court-approved development plans were apparently not adhered to, with the installation of a large kitchen exhaust chimney.

Opposition Leader Peter Cumming called on Cr Quirk to make clear the cost of rent unpaid and when UHFA stopped paying rent.

Cr Cumming also questioned whether the charity still leased a food-vending stall in Brunswick Street mall from the council.

“Labor has questioned the appointment of UHFA from day one,” Cr Cumming said.

“This was an unknown charity that had made virtually no returns to relevant authorities yet they were awarded an opportunity more established charities would give their eye teeth for.

“Last May, Cr Quirk was adamant the rent was being paid in full. Ratepayers deserve to know when the problems started.”

Cr Cumming said he had asked two weeks ago to inspect files on the Engine Room cafe but had not yet been given permission.

The cafe sits close to the river's edge and is a popular location for walkers and cyclists to stop for a coffee.