Later, he worked for railroads in Omaha, Nebraska, and Aurora, Illinois, before joining a Chicago salt distribution company in 1880.

By 1886, he owned the firm, renaming it Joy Morton and Company, and branching out into the distribution and processing of agricultural products in Nebraska and Illinois.

Morton also served on the Chicago Plan Commission for 25 years and was a staunch advocate of inland waterway transportation and building air rights.

His advocacy of air rights in Chicago helped make possible the construction of buildings above railway lines, such as the Merchandise Mart.

They agreed that the Morton Arboretum should exist to display woody plants that grow in temperate zones around the world, to educate the public about them, and to conduct research on their management and preservation.

After his father's death, he hired the architect Jarvis Hunt to redesign and enlarge Arbor Lodge into a 52-room mansion and used it as his family's summer home.