The controlled intercalation of selected species underneath graphene or hexagonal boron nitride (hBN) on a substrate opens new ways for the functionalization and the tuning of properties of these systems. In this work, the case of hBN on rhodium exposed to a low-energy Ar-ion beam [Cun et al., Nano Lett. 2013, 13, 2098–2103] is further considered theoretically. With the help of ab initio molecular dynamics, the structural rearrangements induced by the interaction between the impacting Ar ion and the substrate are investigated. It is shown that the ion can be intercalated and trapped between the metal and hBN by breaking some BN bonds and penetrating the overlayer. The resulting defective structure relaxes quickly, while Ar moves to a stable site where a protrusion appears on top of the characteristic super honeycomb lattice of the nanomesh. The presented results provide a first atomistic description of the complex processes leading to the formation of the, so-called, boron nitride nanotents.