The excess of capping agents used during the synthesis of nanoparticles is usually removed by solvent washing. The influence of the amount of polyvinylpyrrolidone (PVP) capping agent in the catalytic activity of palladium nanocubes was evaluated, after different numbers of washing cycles in the purification step performed after the syntheses of the nanoparticles. The effect of PVP amount on the hydrogenation of unsaturated carbon-carbon bonds was evaluated in terms of kinetic analysis and diffusion experiments. Five different catalysts were prepared utilizing the washing off procedure. All catalysts were characterized by transmission electron microscopy, X-ray photoelectron spectroscopy, small angle X-ray scattering spectroscopy and dynamic light scattering. The reaction presented strong influence by the amount of PVP, which was determined to be due to a balance between the amount of capping agent and the structure of the substrate.