The company confirmed that the bakery, located in the Pueblo Nuevo neighbourhood of Madrid, "was closed and would stay closed".
"The company has put itself at the disposal of the appropriate authorities and has opened an internal investigation into these events," the company said, adding that food safety protocol had been "strictly adhered to" in the establishment.
Granier said that the bakery underwent quarterly inspections, the last having taken place on October 26, when, according to documents released by the company, the branch in question was fumigated.
It was, the company claimed, "an isolated event" and "the 350 Granier establishments in Spain and abroad comply strictly with all food health regulations".
The video has been watched tens of thousands of times since it was uploaded to social media on Saturday, with some comments comparing the rats to the gourmet food-loving rodents in the Disney film, Ratatouille.