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Unveiling the interplay of semiconducting organic molecules with their environment, such as inorganic materials or atmospheric gas, is the first step to designing hybrid devices with tailored optical, electronic or magnetic properties. The present article focuses on a double-decker lutetium phthalocyanine known as an intrinsic semiconducting molecule, holding a Lu ion in its center, sandwiched between two phthalocyanine rings. Carrying out experimental investigations by means of electron spectroscopies, X-ray diffraction and scanning probe microscopies together with advanced ab initio computations, allows us to unveil how this molecule interacts with weakly or highly reactive surfaces. Our studies reveal that a molecule–surface interaction is evidenced when molecules are deposited on bare silicon or on gold surfaces together with a charge transferred from the substrate to the molecule, affecting to a higher extent the lower ring of the molecule. A new packing of the molecules on gold surfaces is proposed: an eclipse configuration in which molecules are flat and parallel to the surface, even for thick films of several hundreds of nanometers. Surprisingly, a robust tolerance of the double-decker phthalocyanine toward oxygen molecules is demonstrated, leading to weak chemisorption of oxygen below 100 K.