Highly active, supported Au-Pd catalysts have been tested for catalyzing benzyl alcohol oxidation in a silicon-glass micropacked bed reactor. The effects of Au-Pd composition and anion content during catalyst preparation on catalyst deactivation were studied, and a relationship between the deactivation rate and the amount of Cl- and Au used in the catalyst formulation was found. While Au AIDS in enhancing the selectivity to the desired product and the Cl- ions help the formation of uniform 1-2 nm nanoparticles, higher amounts of Au and Cl- become detrimental to the catalyst stability once a certain amount is exceeded. Loss of small (1-2 nm) metal nanoparticles was evident in all catalysts studied, accompanied by agglomeration and the formation of larger >10 nm particles. A secondary deactivation mechanism characterized by the formation of an amorphous surface film was observed via transmission electron microscopy in catalysts with high Cl- and Au and was associated with the detection of carbon species on the catalyst surface using Raman spectroscopy.