Fire is endemic to many of the plant communities found in Poly Canyon. However, there are few records of fire in the canyon. Because indigenous peoples of other continents used fire to reduce the density of brush and to encourage the growth of certain plants for forage by the animals they hunted, it has been assumed that California's native peoples also did so. California's native peoples used fire to reduce the density of the brush. They also set fires to encourage the growth of certain plants, particularly in grasslands. The stems of certain grasses were valuable for basketry. Seeds of some grasses were important food either for the people or for the animals they hunted. Chumash knew that a light burn would eliminate competition for the oak seedlings and saplings whose acorns they would eventually harvest. This also could apply to the seeds and fruits of chia and islay, both of which were highly valued by the Chumash. Whether local Chumash practiced this in Poly Canyon has not been determined.

Spaniards also used fire, though for a different purpose. They burned areas, especially chaparral and coastal scrub, in order to convert the land to agricultural use. If this was done in Poly Canyon, the land's main use would have been pastures for livestock as it is too steep and hilly, and water is available too intermittently to cultivate crops on a large scale.

Available records do not report more than two fires in the canyon over the last one hundred or so years. The first, on June 9, 1975, consumed approximately 15 acres of chamise chaparral located "900 feet to the left [east] of the 'P'."

The second was the Highway 41 or Cerro Alto fire of mid-August 1994 that burned along the northern and northeastern edges of the canyon (the hill and ridge above the train tracks and just below the tracks to the road). Numerous scientific studies of these burned areas have begun.