Metal nano-aerogels combine a large surface area, a high structural stability, and a high catalytic activity towards a variety of chemical reactions. The performance of such nanostructures is underpinned by the atomic-level distribution of their constituents. Yet monitoring their sub-nanoscale structure and composition to guide property optimization remains extremely challenging. Here, we synthesized Pd nano-aerogels from a K2PdCl4 precursor and two different NaBH4 reductant concentrations in distilled water. Atom probe tomography reveals that the aerogel is poly-crystalline and that impurities (Na, K) are integrated from the solution into grain boundaries. Ab initio calculations indicate that these impurities preferentially bound to the Pd-metal surface and are ultimately found in grain boundaries forming as the particles coalesce during synthesis, with Na atoms thermodynamically equilibrating with the surrounding solution and K atoms remaining between growing grains. If controlled, impurity integration, i.e. grain boundary decoration, may offer opportunities for designing new nano-aerogels.