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We use in situ scanning tunneling microscopy (STM) to investigate intercalation of the ferromagnetic 3d metals Ni and Fe underneath a graphene monolayer on Rh(111). Upon thermal annealing of graphene/Rh(111) with the deposited metal on top, we observe the formation of epitaxial monatomic nanoislands grown pseudomorphically on Rh(111) and covered by graphene. The size and shape of intercalated nanoislands is strongly influenced by the local spatial variation of the graphene -Rh bonding strength. In particular, the side length of the intercalated nanoislands shows maxima around discrete values imposed by the periodicity of the graphene moiré. Intercalation can be performed efficiently and without any visible damage of the graphene overlayer in the studied temperature range between 670 and 870 K. We identify the main intercalation path to be via diffusion through pre-existing lattice defects in graphene, accompanied by the second mechanism which is based on the material diffusion via metal-generated defects followed by the defect healing of the graphene lattice. We deem these graphene-capped and sharply confined ferromagnetic nanoislands interesting in the fields of spintronics and nanomagnetism.