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Ruthenium nanoparticles have been prepared by hydrogenation of the complex Ru(COD)(COT) (COD = 1,5‐cyclooctadiene, COT = 1,3,5‐cyclooctatriene) in the presence of i) heavily fluorinated solid compounds as stabilizers (para‐bis(perfluorooctyl)benzene, 2,4,6‐tris(perfluorooctyl)aniline, and the non‐functionalized 11H,11H,12H,12H,13H,13H,14H,14H,15H,15H,16H, 16H‐perfluorohexacosane (C10F21‐(CH2)6‐C10F21)); and ii) the liquid 1H,1H,2H,2H‐perfluorodecylamine. The particles have been characterized by IR spectroscopy, elemental analysis, transmission electron microscopy (TEM), high‐resolution TEM, wide‐ and small‐angle X‐ray scattering (WAXS and SAXS), and scanning electron microscopy with a field‐emission gun (SEM‐FEG). TEM images indicate the presence of aggregated small nanoparticles with a regular mean size of ca. 3 nm. These nanoparticles display the hexagonal close‐packed structure of bulk ruthenium, as shown by WAXS analysis. HRTEM and SEM‐FEG analyses reveal the tendency of the particles to self‐assemble into superstructures (spheres) that can be more or less well defined depending on the fluorinated compound and/or the reaction conditions. This behavior has been confirmed in one case by SAXS measurements attesting the presence of small nanoparticles that are closely packed into clusters.