The physicochemical properties of broad bean paste koji made from extruded and traditional steam-cooked raw materials were investigated by scanning electron micrographs (SEM), confocal laser scanning micrographs (CLSM), circular dichroism (CD) and Molecular weight (Mw) analysis. The results showed that the protease activity of koji made from the extruded materials was higher than that of the traditional cooking method. A network porous structure in the extruded samples was observed by SEM. Furthermore, the CLSM results showed that the starch of the extrudate was embedded well in its protein network. CD spectroscopy implied that the α-helix decreased while the β-turn and random coil increased after both treatments. Mw analysis determined that the starch molecules were degraded during extrusion, the proportion of micromolecules was more in the extruded samples than in the steam-cooked samples. However, the chain length distribution of starch exhibited no significant difference between the extruded and steam-cooked broad beans.