Dewetting or agglomeration is a crucial process in material science since it controls the stability of thin films or can be used for film nanostructuration by formation of islands. The models developed for dewetting usually assume diffusion at the interface and/or at the surface but no direct evidence of such diffusion was demonstrated. Moreover, these models are usually dealing with elemental materials and not with compounds in which several elements can diffuse. The mechanisms behind agglomeration of polycrystalline compounds thin film are still not fully understood. In this work, Si isotope multilayers coupled with atom probe tomography (APT) are used to reveal the agglomeration mechanism of NiSi, a binary compound. The diffusion of Si, the less mobile species in NiSi, at the NiSi/Si interface is demonstrated through comparison between the three dimension redistribution of the Si isotopes determined by APT and models taking into account grooving and agglomeration. The implication for the understanding and control of agglomeration in poly-crystalline compound thin films are highlighted.