Research and teaching at the Institute of Archaeology are organized into several departments, subdivided by chronological periods: Prehistoric archaeology, Biblical Archaeology and Classical archaeology (with an additional sub-department in medieval Islamic archaeology), and a department of Civilizations of the Ancient Near East.

Sevaral labs operate at the Institute, which deal in a wide variety of archaeological materials and research fields. These include the Computational Archaeology Labratoty, a Conservation and Restoration Lab, the Laboratory for Archaeological Materials and Ancient Technologies, and the Zooarchaeology Lab (at the Givat Ram Campus)