Descriptions by early white settlers demonstrate its continued use by the Dakota in the 19th century: Charles La Trobe described a tomb of an Indian chief at the summit of the hill in 1832–1833,[2] French explorer Joseph Nicollet described a "great gathering of people" on the hill and observed a Dakota medicine dance in 1837,[4] and Mary Henderson Eastman described Pilot Knob as "proud to be the burial place of her warrior children...."[5] French settlers called the hill La Butte des Morts (Knoll of the Dead).

These observations have been supported by a modern-day analysis of skeletal remains found on the hill which included individuals of both Native American and European origin.

In 1848, Illinois Senator Stephen Douglas suggested that Mendota Heights be the location of Minnesota’s territorial capital with the public buildings on Pilot Knob.

[7] The proposal was criticized by members of the Dakota and Ojibwe communities, archaeologists, environmentalists, historians, and local residents, and led to the formation of the nonprofit Pilot Knob Preservation Association.

[12] The purchase was a collaborative effort by the Trust ($120,000), the city of Mendota Heights ($400,000), the Minnesota Department of Natural Resources ($1,050,000), Dakota County ($400,000), and the Pilot Knob Preservation Association.

[11] The 25 acres (10 ha) (plus 9 already owned by the city) is undergoing restoration to oak savanna, led by Great River Greening, a local non-profit.

[7] In the opposite direction, Pilot Knob Road continues south to Dakota County 50/212th St W, on the border between Lakeville and Farmington.