A pretreatment method using aqueous ammonia was investigated with the intent of minimizing the liquid throughput. This process uses a flow-through packed column reactor (or percolation reactor). In comparison to the ammonia recycle percolation (ARP) process developed previously in our laboratory, this process significantly reduces the liquid throughput to one reactor void volume in packed bed (2.0-4.7 mL of liquid/g of corn stover) and, thus, is termed low-liquid ARP (LLARP). In addition to attaining short residence time and reduced energy input, this process achieves 59-70% of lignin removal and 48-57% of xylan retention. With optimum operation of the LLARP to corn stover, enzymatic digestibilities of 95, 90, and 86% were achieved with 60, 15, and 7.5 filter paper units/g of glucan, respectively. In the simultaneous saccharification and fermentation test of the LLARP samples using Saccharomyces cerevisiae (NREL-D(5)A), an ethanol yield of 84% of the theoretical maximum was achieved with 6% (w/v) glucan loading. In the simultaneous saccharification and cofermentation (SSCF) test using recombinant Escherichia coli (KO11), both the glucan and xylan in the solid were effectively utilized, giving an overall ethanol yield of 109% of the theoretical maximum based on glucan, a clear indication that the xylan content was converted into ethanol. The xylooligomers existing in the LLARP effluent were not effectively hydrolyzed by cellulase enzyme, achieving only 60% of digestibility. SSCF of the treated corn stover was severely hampered when the substrate was supplemented with the LLARP effluent, giving only 56% the overall yield of ethanol. The effluent appears to significantly inhibit cellulase and microbial activities.