Thiolate self-assembled monolayers (SAMs) are often used to modify surface properties, including catalytic activity. These SAMs can also induce reconstruction of some metallic surfaces. Here we show, through formation and subsequent removal of thiolate SAMs from Au polycrystalline electrocatalysts, that irreversible changes to the underlying metal surface can lead to significant changes in catalytic properties, irrespective of specific interactions that might occur between thiolate molecules and various reactants. Using underpotential deposition of Pb as a surface probe, we find that across a range of different thiolates, SAMs tend to increase the proportion of (111)-facets on Au, but they simultaneously increase the defect density upon these and other facets. These changes lead to delayed onset but higher maximum activity toward formic acid oxidation, which is interpreted in terms of both the density of appropriate active site ensembles and changes to the binding isotherm for site-blocking hydroxyl species. The impacts of reconstruction are further illustrated through measured shifts in selectivity for electroreduction of crotonaldehyde, with reconstructed catalysts changing the favored product from butanal to crotyl alcohol. Thus, complex surface reorganization may play a significant role in catalytic behaviors of thiol-coated SAMs as well.