In this paper, the authors describe the conditions under which Fe forms encapsulated nanocrystals beneath the surface of graphite, and they characterize these islands (graphite + Fe) thoroughly. The authors use the experimental techniques of scanning tunneling microscopy (STM) plus x-ray photoelectron spectroscopy (XPS) and the computational technique of density functional theory (DFT). Necessary conditions for encapsulation are preexisting ion-induced defects in the graphite substrate and elevated deposition temperature of 875–900 K. Evidence of encapsulation consists of atomically resolved STM images of a carbon lattice, both on top of the islands and on the sloping sides. The nature of the images indicates that this carbon lattice corresponds to a graphene blanket consisting of more than one graphene sheet that drapes continuously from the top of the island to the graphite substrate. The formation of iron carbide is not observed based on XPS. Shapes of the island footprints are consistent with metallic Fe, predominantly in the hcp or fcc form, though larger islands tend toward bcc. Island structures with hexagonally close-packed lateral hcp or fcc planes are stabilized by their excellent lattice match with the graphite substrate. Evolution of island density with prolonged deposition time provides evidence of coarsening, perhaps via Smoluchowski ripening. The encapsulated Fe clusters are stable in air at room temperature, protected by smaller Fe clusters that decorate defect sites and block permeation of gases. DFT shows that two configurations of Fe are more stable within the gallery than adsorbed on top of the surface: a single atom of Fe and a film (slab) of metallic Fe. Comparison with other metals shows that encapsulated Fe is similar to Cu but dissimilar to Ru or Dy, leading the authors to conclude that carbon dissolution in the metal does not play a role in encapsulation.