In this paper, we report on the effects of loblolly pine residue variability on material throughput, pilot plant uptime, operator intervention, product yield, and product quality for grinding, fast pyrolysis, and hydrotreating operations. Preprocessing throughput using a hammer mill varied between 31 and 48% of nameplate capacity (5 tons/h). Grinder overloads in the size reduction step were more prevalent for lower ash and higher moisture materials. Fast pyrolysis throughput varied between 57 and 72% of nameplate capacity (20 kg/h), and bio-oil yields varied between 46 and 53% (feedstock carbon to oil, dry basis). During fast pyrolysis operations, downtime was caused by bridging in the feed and char removal systems and plugging in the condensation system. Cohesion of feedstock and char leading to system plugging was less frequent for higher ash feedstocks, and differences in condenser plugging behavior between high and low ash feedstocks were observed. The catalyst stability of the bio-oil stabilization step was strongly dependent on the sulfur content in the bio-oil, which was higher for the high-ash residue oils. Lower moisture content in the starting biomass was consistent with lower sulfur content in bio-oil. Yields and properties of hydrotreated fuel products showed minimal deference among the bio-oils.