Two fire engines attended the Newburn Industrial Estate after there was a fire in one of the ovens at the factory, which Warburtons bought from North East Bakery after it went into administration in 2010.
Staff were evacuated as a standard safety procedure.
A spokeswoman for Warburtons said the bakery, which was rebranded from Newburn Bakehouse to Warburtons Gluten Free in January and makes the company’s free-from ranges, was now operational again.
In July, Warburtons announced the launch of several new gluten-free wraps, including a beetroot wrap, as part of a wider overhaul of its gluten-free ranges.