Aza-BODIPY are a class of organic fluorescent dyes which have recently become interesting for organic photovoltaics because of their strong tuneable infrared absorption and their high stability. We investigated two molecular species consisting of two aza-BODIPY core units bound to one central metal atom by low temperature STM/STS and ab initio DFT calculations. The aim of this study was to find out how the different metal atoms (Co, Zn) influence the properties of the organic molecules. Because of steric hindrance among the aza-BODIPY ligands these molecules have a three dimensional structure. That is why the inner structure of the molecule could not be imaged by STM. We evaporated the aza-BODIPY onto a Ag(110) surface, separately. Both molecular species show two different adsorption geometries and are topographically identical. In the STS measurements of the Co-aza-BODIPY different spectra were obtained for the same position on the same molecule. One part of the spectra was very similar to those measured on Zn-aza-Bodipy, while the other spectra showed additional states near the Fermi level. DFT calculations indicate that the changes in these Spectra are related to the spin crossover effect.