Large-scale fabrication of metal cluster layers for usage in sensor applications and photovoltaics is a huge challenge. Physical vapor deposition offers large-scale fabrication of metal cluster layers on templates and polymer surfaces. In the case of aluminum (Al), only little is known about the formation and interaction of Al clusters during sputter deposition. Complex polymer surface morphologies can tailor the deposited Al cluster layer. Here, a poly(methyl methacrylate)-block-poly(3-hexylthiophen-2,5-diyl) (PMMA-b-P3HT) diblock copolymer template is used to investigate the nanostructure formation of Al cluster layers on the different polymer domains and to compare it with the respective homopolymers PMMA and P3HT. The optical properties relevant for sensor applications are monitored with ultraviolet-visible (UV-vis) measurements during the sputter deposition. The formation of Al clusters is followed in situ with grazing-incidence small-angle X-ray scattering (GISAXS), and the chemical interaction is revealed by X-ray photoelectron spectroscopy (XPS). Furthermore, atomic force microscopy (AFM) and field emission scanning electron microscopy (FESEM) yield topographical information about selective wetting of Al on the P3HT domains and embedding in the PMMA domains in the early stages, followed by four distinct growth stages describing the Al nanostructure formation.