The formation of a high quality interface between metallic and organic semiconducting thin films is critically important in achieving high-performance organic electronics devices. In this regard, the importance of understanding the multifaceted issue of structure damage incurred to organic films by the evaporated metal atoms cannot be overstated. In the present study, we have investigated the change of a structurally ordered, organic semiconducting (o.s.) thin film of 5,11-bis(triethylsilylethynyl)anthradithiophene (TESADT) effected by gold atoms by means of synchrotron-based soft X-ray spectroscopies including ultraviolet photoemission spectroscopy (UPS) and X-ray photoemission spectroscopies (XPS) with imaging capability, near edge X-ray absorption fine structure (NEXAFS) spectroscopy, and atomic force microscopy (AFM). This work shows that gold atoms readily diffuse into the organic films and nucleate into nanometer-size clusters, damage chemical structure, destroy structural ordering of the organic films, and shift relevant core level binding energy in accord with the expected interfacial band bending. Additionally, the patterned deposition performed via shadow mask is not reliable in confining Au deposit to the designated region due to the rapid diffusion of Au atoms. As a result, the real Au contacts should be treated as morphologically complicated gold films residing on top of structurally disordered organic film interspersed with Au clusters.