Mount Jefferson is a stratovolcano, made up of basaltic andesite, andesite, and dacite overlying basaltic shield volcanoes, with andesite and more silicic (rich in silica) rock forming the majority of the mountain. Rhyolite from the Quaternary can also be found at Jefferson, though it is not commonly found within the major volcanic centers of the Oregon Cascades. The volcano constitutes a small stratovolcano within the Cascades, with a current volume of , though prior to erosion and other alterations over time, it may have been as large as in volume at one time. Mount Jefferson has been significantly altered by erosion, and represents one of the most eroded stratovolcanoes in the state of Oregon. Glacial motion during the Pleistocene decreased the summit's elevation by a few hundred feet and formed a cirque (an amphitheatre-like valley carved by glacial erosion) on the western side of the volcano. This feature, known as the West Milk Creek cirque, includes the two Milk Creek glaciers and extends into the interior of Mount Jefferson, exposing tephra and pyroclastic rock in the main volcanic cone. The final two advances of glaciers during the Pleistocene removed about a third of the volcano's original volume, decreasing the overall elevation by . Currently, the Whitewater Glacier and the Milk Creek glaciers erode the mountain's eastern and western flanks, respectively, and are likely to gradually form a cleft between the northern and southern horns of the summit.