The inclusion of sunflower meal to substitute soybean meal protein was examined for its effect on the physical properties and microstructure of extrudates processed under two different preconditioner moistures. Two diets were formulated by substituting soybean meal with sunflower meal at levels of 0 and 50%. The two diets were processed under two preconditioner moisture levels of 15 and 20% to produce four different extrudates. Interaction between preconditioner moisture and the substitution factors showed a highly significant effect on expansion percentage, bulk density and apparent porosity % of the extrudates, while no significant effect was detected on maximum oil absorption and fat leakage. The extrudates of sunflower meal appear less expanded, with less diameter and apparently darker than soybean meal extrudates. The surface morphology of sunflower meal pellets extruded with high preconditioner moisture was more compact and less cracked with fewer pores. It seems that the cellulose of the extrudates increased with more inclusion of sunflower meal, affecting the physical probability and microstructure.