Ten firefighters are continuing to dampen down the flames and are checking for hot spots at a building housing recycled waste and carpets in Saltney.
It started shortly after 11:30 BST on Wednesday and crews from six fire stations were sent to the scene at the height of the fire.
Workers at 11 industrial units had to be evacuated.
Fire crews are still at the scene of a blaze which broke out at a storage warehouse in Flintshire.