The housing and homelessness charity Shelter said their shop on Union Street had been “completely destroyed”.
Shelter Scotland director Alison Watson said the charity was “heartbroken”.
“Crucially, everyone who was in our Union Street shop is safe,” she added.
“The shop was evacuated as soon as the alarm was raised, and our team are now being supported by colleagues.”
On Monday, the first minister said the government recognised that the fire was an “unexpected and extraordinary” incident in the city that would impact businesses that had lost their premises, or had just lost footfall since part of the city has been closed down.
He added: “We do now have to think about how we support those local businesses, how we make sure there is safety on the site, it’s secured, how we can get travel back active again.”