Catalytic fast pyrolysis (CFP) is a technology option for producing advanced biofuels from hydrocarbon-rich biocrude intermediates. The relatively high oxygen content of biocrudes compared to petroleum intermediates increases hydrogen consumption and the lower thermal stability accelerates catalyst deactivation and reactor fouling hindering the adaptation of hydrotreating technology for biocrude upgrading into biofuels. In this study, four chemically different biocrude feeds were upgraded in a pilot scale hydroprocessing unit at similar process conditions using a commercial hydrodeoxygenation (HDO) catalyst. The biocrude feeds and hydrotreated products were characterized using standard ASTM procedures and advanced analytical techniques (GCxGC-FID and GCxGC-MS). HDO catalyst activity was monitored by changes in physical properties and chemical composition of the upgraded products as a function of time on stream. Aliphatic acids, ketones, aldehydes, and furan derivatives were completely converted during the hydrotreating tests while the concentration of aromatics, aliphatic hydrocarbons and phenolics increased during the hydrotreating tests. The oxygen content, nitrogen content, specific gravity, viscosity and the heavy end of the boiling point range (determined by simulated distillation) of the upgraded products increased with increasing time on stream during hydrotreating. The deactivation rate was the lowest for the biocrude feed that contained the most aliphatic and aromatic hydrocarbons and was the highest for the biocrude feed that had the most anhydrosugars. Overall, the HDO deactivation rate correlates with the total amount of oxygen in the feed (17 wt% to 29 wt%, on a wet basis).