The effects of soybean by-products — soybean hulls (SH), soybean meal (SM) and raw soybean seeds (RSS) — on the rumen microbial population and fermentation were studied. The concentration of total rumen bacteria was greater (P = 0.06) for the SH and SM diets as compared to RSS. The concentration of cellulolytic bacteria tended to be higher with the SH and SM diets. Protozoal concentrations were significantly lower for the SH diet at feeding (T0, P < 0.05). Generic composition of protozoa was distinctly different among the soybean by-products. The composition of protozoa at T0 and 3 h (T3) for the SH diet group primarily consisted of vestibuliferids and Entodinium sp. with only 1% of protozoa from different genera present in the 6 h (T6) samples. The protozoa composition was more diverse with the SM and RSS diets, in that the “Others” types of entodiniomorphs included the genera Epidinium, Ophryoscolex, Metadinium, and Diplodinium. With the SH treatment, total VFA was greater and ruminal pH and acetate:propionate ratio were lower compared with the SM and RSS diets. Supplementation with all the soybean by-products modified both the microbial population and fermentation products and had an increased total dry matter intake in grazing dairy cattle.