We present an extensive structural analysis of hybrid architectures prepared by the “soft” incorporation of gold nanoparticles (AuNPs) within an organic semiconductor matrix of diindenoperylene (DIP). Such “soft” or noninvasive deposition of nanoparticles within organic semiconducting host matrices not only minimizes the influence of the deposition process on the order and properties of the organic host molecules, but also offers additional control in the process of incorporation. The hybrid structures were characterized by X-ray scattering techniques including grazing incidence small angle X-ray scattering (GISAXS), grazing incidence X-ray diffraction (GIXD), X-ray reflectivity (XRR), and complemented by atomic force microscopy (AFM), photoluminescence (PL) spectroscopy, and transmission electron microscopy (TEM) measurements. We show that different strategies of incorporating the nanoparticles in the host matrix lead to drastically different structure and morphologies. Particularly remarkable is the morphological change observed in the matrix of DIP as well as the AuNPs due to the influence of organic solvents, as evidenced by TEM tomography measurements, which revealed the exact location of the AuNPs within the organic host. It is also demonstrated that AuNPs can be successfully used as tunable templates for the growth of the organic semiconductors with desired island sizes and distances.