Pretreatment and densification of agricultural residues at regional depots can simplify feedstock supply logistics for the production of biofuels in commercial biorefineries. We have previously reported the performance of a laboratory-scale (5 L) packed-bed ammonia fiber expansion (AFEX) reactor system, which showed significant promise for biomass pretreatment at distributed depots. In this paper, we describe the performance of a 90-fold larger pilot-scale packed-bed AFEX-reactor system, used to produce over 1,500 batches (similar to 36 tons) of pretreated crop residues over a 5-year period. Virtually all unreacted ammonia was successfully removed from the biomass, and 76% of the ammonia was recycled and reused. Pretreatment performance at pilot scale was comparable to laboratory-scale, averaging 74% glucose and 75% xylose yield in a standard test compared with 71% and 73%, respectively. Other operating and maintenance aspects are also discussed.