Subtle changes in the geometric and electronic properties of supported molecules, with a potential impact on the functioning of molecular devices, can typically be imaged by scanning probe microscopy, but their exact origin and nature often remain unclear. Here we show explicitly that the symmetry reduction of iron phthalocyanine upon adsorption on Cu(111) can be observed not only in scanning tunneling microscopy, but also in core-level spectroscopy, and that it is related to nonisotropic charge transfer into the two principal molecular axes, but in combination with topographic influences.