This paper describes the results of an investigation of the evolution and the reconstitution of core-shell assembled gold nanoparticles in electrocatalytic activation for methanol electrooxidation. The aim is to probe the structural and morphological reconstitution upon the catalytic activation. Gold nanoparticles of 2-nm core size are linked by 1,9-nonanedithiolates into a network thin film on planar substrate, and are explored as a model system of core-shell nanostructured catalysts. This system is probed using three characterization techniques: electrochemical quartz-crystal nanobalance (EQCN), infrared reflection spectroscopy (IRS), and atomic force microscopy (AFM). The EQCN detected two types of mass changes across the nanostructured catalysts. One corresponds to shell desorption upon the oxidative potential-driven activation, and the other relates to the formation of surface oxygenated species during the catalytic oxidation of methanol. IRS provided two pieces of evidence for the shell reconstruction upon the activation. One is indicative of the desorption of the shell thiolates, and the other relates to the interparticle, electronic effect. AFM revealed morphological changes of the nanoparticle assemblies in terms of the film smoothness and the particle size that are dependent on the thickness of the nanoparticle assembly. While thick films displayed enlarged nanoparticle features, thinner films exhibited a relatively smaller evolution. The catalytic activity is associated with the partial or even complete desorption of network shell components accompanied by the formation of surface oxygenated species, a reconstitution process that may have important implications to the delineation of design and preparation parameters of nanoporous and highly active nanoscale catalysts.