Last month's blast at Wood Treatment Ltd reduced the Bosley mill to rubble.
Will Barks, Derek Moore and Dorothy Bailey were identified as victims, but Jason Shingler, 38, remains missing.
While Cheshire Fire and Rescue Service say they have now handed the investigation over to police, a search and rescue team will stay at the site.
Small fires were still burning at the site until last week, but a fire service spokesman said these have now been extinguished.
He added that crews would return to the area if any hidden or smouldering fires were uncovered.
Temperatures reached 1,000C in the blast and it was described by rescue workers as the "worst incident of its kind" in a decade.
The Bosley Disaster Appeal Fund has raised more than Â£53,000 for the families of the victims and workers left without jobs.
In a statement last week the mill's owners said they "could not predict" when the factory would be operational again.
An investigation into the cause of the explosion continues.
Firefighters have left the site of the Cheshire wood flour mill which was destroyed in an explosion that left three people dead and a fourth missing.