Methods of assembling a stiffened composite structure include loading, with a stiffener loading tool, a respective stiffener from a supply of stiffeners onto an inner mold line layup mandrel; repeating the loading to load a plurality of stiffeners onto the inner mold line layup mandrel; and following the repeating, affixing a respective skin segment from a supply of skin segments to the plurality of stiffeners loaded on the inner mold line layup mandrel to form at least a portion of the stiffened composite structure. Systems for assembling stiffened composite structures include a supply of stiffeners; an inner mold line layup mandrel; and a stiffener loading tool configured to load the respective stiffener onto the inner mold line layup mandrel.