The use of stabilizers is an essential part of colloidal catalyst preparation, however their impact on catalytic behavior is challenging to elucidate. This report evaluates three commonly used nanoparticle (NP) stabilizing ligands, oleylamine (OAm), dodecanethiol (DDT) and the polymer polyvinylpyrrolidone (PVP). Stabilizing ligands are removed using thermal and chemical pre-treatments and the surface chemistry of the NPs is assessed using X-ray photoelectron spectroscopy (XPS). The method of ligand removal significantly altered the catalytic behavior of colloidal NPs. Chemical treatment was less effective in completely removing the capping ligands, however catalytic activity could be improved by partial ligand removal. Thermal pre-treatment decreased the activity of all the catalysts, even when the catalyst diameter and Pd surface chemistry was reasonably preserved. XPS analysis further revealed changes in the interfacial chemistry of the treated catalysts such as the formation of oxidized sulfur species formed during annealing DDT-Pd NPs and conformational changes in PVP capping ligands as a result of thermal treatment.