The formation of metal/organic interfaces is a complicated process involving chemical interaction, physical nucleation and diffusion, and thin film growth. It is closely related to the performance of organic electronic devices. To understand this process, we investigate the system of aluminum (Al) and tris(8-hydroxyquinolinato)aluminum (Alq3) as a model, owing to the well-known strong chemical interaction between both and their close technological relevance to organic light emitting devices. By using grazing small angle incidence X-ray scattering (GISAXS), we follow the Al thin film development on top of Alq3 during radio frequency (rf) sputter deposition in real-time and without interrupting the growth process. Three growth stages have been clearly distinguished: Al diffusion into Alq3, Al/Alq3 complex agglomeration and self-assembled Al pillar nanostructure thin film development. Thus in situ GISAXS yields the fundamental insights into the formation of the metal/organic interface for small organic semiconductor devices, prepared via vacuum based deposition techniques.