He worked as a general assignment reporter for a succession of newspapers throughout the United States – including the Superior Express, the Wyoming Tribune-Eagle, the Savannah Morning News, The Salt Lake Tribune, the San Francisco Chronicle and The Arizona Republic—before leaving daily journalism altogether to write books.

Uranium was praised by The New York Times and Washington Post, and by The Daily Show host Jon Stewart, who called it “crazy, fascinating.” The book won the 2010 Science Writing Award from the American Institute of Physics.

Beginning in 2014, Zoellner was instrumental in gathering support from the Museum of Moab, San Juan County, the Bureau of Land Management, and Mark Steen—son of Charles Steen—for a historic marker commemorating Utah's uranium heritage.

The manuscript was finished in slightly under 100 days and the resulting book, A Safeway in Arizona: What the Gabrielle Giffords Shooting Tells Us About the Grand Canyon State and Life in America (Viking/Penguin, 2012), was published to mixed reviews.

The Boston Globe praised it as “a masterly work of reporting, historical analysis, and sly cultural criticism,”[9] but other reviewers faulted the book for its conclusion that Giffords’ attempted killer had been influenced by a hateful climate in Tucson preceding the 2010 midterm Congressional elections.

The book was reported via a series of rail journeys in Britain, Spain, Russia, China, India, Peru and across the U.S. and has been praised as “an exuberant celebration” by Booklist, "wonderful" by The Washington Post,[10] "spirited and big-hearted," by the San Francisco Chronicle[11] and "engaging" and "keenly observed" by The New York Times'.

[19] In May 2020, Zoellner published Island on Fire: The Revolt That Ended Slavery in the British Empire (Harvard University Press, 2020), a day-by-day account of the Baptist War led by Samuel Sharpe in 1831–1832.

"[25] In 2024, just before Democratic Presidential candidate Kamala Harris chose her running mate, Zoellner penned a measured panegyric on Arizona Senator Mark Kelly, lauding his virtues as a meticulous former astronaut and pragmatically centrist politician.