Most of John Hanson Mitchell's work is focused on a square mile tract of land known as Scratch Flat, located about thirty-five miles north-west of Boston. Mitchell has used this anomalous landscape of rolling hills, farms, forests and encroaching suburbs to explore his continuing interest in natural and human history and the whole question of place in human cultures, both native and European. Best known of this series of books is the first, Ceremonial Time:Fifteen Thousand Years on One Square Mile. The latest book in the group is An Eden of Sorts: The Natural History of My Feral Garden. All of these books have been collected together in a series known as The Scratch Flat Chronicles.

Other books explore the relationship between culture, nature, and place both here and abroad. These works deal with such disparate subjects as the relationship between Italian gardens and the American wilderness and the role of the sun in various cultures, outlined in the book Following the Sun, a 1500 mile bicycle journey he made from Cadiz in Spain, north to the Isle of Lewis in the Outer Hebrides. His last book among these is The Paradise of all These Parts, a natural history of the little peninsula that became the city of Boston.