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.