He worked on projects in New York, the Southwest and, most notably, the Nacoochee Mound in northeastern Georgia.
In 1895, he was contracted by the American Museum of Natural History in New York to continue his work at the site located in the Tottenville section of Staten Island.
From 1896 to 1900, Pepper led the excavation of the Pueblo Bonito great house in Chaco Canyon, New Mexico.
In 1915, Pepper he traveled to Georgia to explore the Nacoochee Mound in the state's historic Cherokee region, on an excavation sponsored by the Heye Foundation, Museum of the American Indian and Bureau of American Ethnology.
[1] In 1918, George Gustave Heye, Hodge, and Pepper published their findings as The Nacoochee Mound Report (scanned copy available at the Internet Archive).