He graduated from Columbia College, where he showed an interest in science and was taught natural history by David Hosack, founder of Elgin Botanical Garden.

[1] John Le Conte's older brother Louis inherited the family plantation, Woodmanston, near Midway in Georgia.

An early ambition to publish an American flora was partially pre-empted when Stephen Elliott began A Sketch of the Botany of South-Carolina and Georgia.

Le Conte's primary interests were zoological, and he co-authored with Jean Baptiste Boisduval a book on insects, Histoire général et iconographie des lepidoptérès et des chenilles de l’Amerique septentrionale (that is, "General history and illustrations of the Lepidoptera and caterpillars of North{ern} America"), which was published at Paris.

John Eatton Le Conte was a fellow of the Linnean Society of London and served as vice-president of the Lyceum of Natural History of New York.

[4] John Eatton Le Conte married Mary Ann Hampton Lawrence on July 22, 1821, in New York.

Their son John Lawrence Le Conte, who became one of the USA's most important early entomologists, was born on May 13, 1825, in New York.