Kelly Knudson's research focuses on political integration and the intersections of different social identities in the pre-Columbian Andes of Bolivia, Peru and Chile.

Knudson directs the Archaeological Chemistry Laboratory at ASU where she and her research team apply biogeochemistry to anthropological research questions. She is also the director of the ASU Center for Bioarchaeological Research.

Knudson's transdisciplinary approach to anthropology is also reflected in her approach to undergraduate and graduate teaching. Whenever possible, she emphasizes hands-on learning experiences in archaeology, archaeological chemistry and bioarchaeology.