Pretreatment based on aqueous ammonia was investigated under two different modes of operation: soaking in aqueous ammonia and ammonia recycle percolation. These processes were applied to three different feedstocks with varied composition: corn stover, high lignin (HL), and low lignin (LL) hybrid poplars. One of the important features of ammonia-based pretreatment is that most of the hemicellulose is retained after treatment, which simplifies the overall bioconversion process and enhances the conversion efficiency. The pretreatment processes were optimized for these feedstocks, taking carbohydrate retention as well as sugar yield in consideration. The data indicate that hybrid poplar is more difficult to treat than corn stover, thus, requires more severe conditions. On the other hand, hybrid poplar has a beneficial property that it retains most of the hemicellulose after pretreatment. To enhance the digestibility of ammonia-treated poplars, xylanase was supplemented during enzymatic hydrolysis. Because of high retention of hemicellulose in treated hybrid poplar, xylanase supplementation significantly improved xylan as well as glucan digestibility. Of the three feedstocks, best results and highest improvement by xylanase addition was observed with LL hybrid poplar, showing 90% of overall sugar yield.