After the war, John settled in Texas county, Missouri and married Rosanna Wiltshire, daughter of Samuel R. Wiltshire. He had met Samuel Wiltshire at some time during the war and travelled to Missouri to see his friend. He ended up staying and marrying Samuel's daughter Rosanna on June 18, 1886.

John Fowler is buried at the Boone Creek Cemetery near Licking, Texas county, Missouri along with his wife, Rosa, his father-in-law and wife, and several of John's children.