Hydrogen absorption by a Pd capped thin Mg2Ni film results in the nucleation of the Mg2NiH4 phase at the film/substrate interface and thus induces a self-organized two-layer system. This leads to the optical black state in Mg2Ni thin films upon hydrogenation. This unusual hydrogenation behaviour is completely unexpected since the hydrogen enters through the top film surface. To explain the nucleation of Mg2NiH4 close to the substrate/film interface we performed scanning tunneling microscopy (STM) on as-prepared Mg2Ni films with various thicknesses (20–150 nm). For films thinner than 50 nm, the film consists of small grains and clusters of small grains whereas on further growth the grain size increases and a columnar microstructure develops. We propose, therefore, that close to the substrate, the relatively porous structure of the film with small Mg2Ni grains locally reduces the nucleation barrier for Mg2NiH4 formation.