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Ru catalyst nanoparticles were encapsulated into the pores of a Cr-based metal-organic framework (MOF)—MIL-101. The obtained material, as well as the non-loaded MIL-101, were investigated down to the atomic scale by annular dark-field scanning transmission electron microscopy using low dose conditions and fast image acquisition. The results directly show that the used wet chemistry loading approach is well-fitted for the accurate embedding of the individual catalyst nanoparticles into the cages of the MIL-101. The MIL-101 host material remains crystalline after the loading procedure, and the encapsulated Ru nanoparticles have a metallic nature. Annular dark field scanning transmission electron microscopy, combined with EDX mapping, is a perfect tool to directly characterize both the embedded nanoparticles and the loaded nanoscale MOFs. The resulting nanostructure of the material is promising because the Ru nanoparticles hosted in the MIL-101 pores are prevented from agglomeration—the stability and lifetime of the catalyst could be improved.