He is the MacArthur Professor of Anthropology at the University of California, Merced where he was previously the Dean of the School of Social Sciences, Humanities, and Arts.
His research themes include the origins of settled village life, human adaptation to high altitude environments, hunting and gathering, and early plant and animal domestication.
Aldenderfer has made important contributions to understanding the Archaic and Formative period peoples of the south-central Andes through active field projects in southern Peru.
He has directed excavation projects at the sites of Asana, Qillqatani, and Jisk'a Iru Muqu, and survey projects in the Osmore valley (Moquegua, Peru) and in river valleys in the Lake Titicaca Basin.
He is currently a Deputy Editor for the open access journal Science Advances.