Thein's artwork is held in the collections of the Albrecht-Kemper Museum of Art in St. Joseph, Mo.; the Sheldon Museum of Art in Lincoln, Neb.; the Joslyn Art Museum in Omaha; Shaanxi Art Museum in Xi'an, China; and the Instituto Guatemalteco Americano, Guatemala City, Guatemala.
For the 23 years before his death in 2023, John Thein worked on a series of paintings addressing the massacre at Wounded Knee, titled “Wounded Knee/the Painted Spirit.”