Metal nanogels combine a large surface area, a high structural stability, and a high catalytic activity toward a variety of chemical reactions. Their performance is underpinned by the atomic-level distribution of their constituents, yet analyzing their subnanoscale structure and composition to guide property optimization remains extremely challenging. Here, we synthesized Pd nanogels using a conventional wet chemistry route, and a near-atomic-scale analysis reveals that impurities from the reactants (Na and K) are integrated into the grain boundaries of the poly crystalline gel, typically loci of high catalytic activity. We demonstrate that the level of impurities is controlled by the reaction condition. Based on ab initio calculations, we provide a detailed mechanism to explain how surface-bound impurities become trapped at grain boundaries that form as the particles coalesce during synthesis, possibly facilitating their decohesion. If controlled, impurity integration into grain boundaries may offer opportunities for designing new nanogels.