After parting from the USGS in 1878, Jackson set up a photography studio, the Jackson Photographic Company, in Denver. His prolific output included portraiture, as well as landscape photography from his travels by rail throughout North America. By the 1890s, economic downturns, advances in technology, and changing public tastes rendered his studio work unprofitable. Relocating to Detroit, Jackson found work with the Detroit Photographic Company (later the Detroit Publishing Company), where he remained for over a quarter century.
In 1893 Jackson became the official photographer for the World Transportation Commission, an initiative to promote American manufacturing and rail transportation worldwide. Led by publicist Joseph Gladding Pangborn, the group traveled across Egypt, Indonesia, Siberia, Australia, Korea, and beyond with the ostensible goal of researching modes of transportation. The Commission's lofty aspirations soon became a 17-month pleasure trip. While it was financially disastrous for the Commission and Jackson, his photographs provide a singular record of time and place.
Jackson’s retirement from professional photography in 1924 hardly slowed his artistic career. In the last two decades of his life, Jackson traded his camera for a brush, producing hundreds of paintings and drawings in watercolor, oil, pencil and ink. These included vignettes from his youth and idealized tableaus of American westward expansion, as well as commissions from the National Park Service. Jackson recreated several of his original Oregon Trail sketches for inclusion in his autobiographies, The Pioneer Photographer (1929, written with Howard R. Driggs) and Time Exposure (1940, written with Karl Brown). He also redeveloped negatives from his expeditions and created hand-tinted slides of his USGS photographs.
Jackson died due to complications from a fall on June 30, 1942, at age 99. Over 125 friends and associates attended his funeral service. Among their number was former National Park Service Director Horace Albright, who referred to Jackson as "the grand old man of Yellowstone."