We review the results of our achievements on thin film processes in organic materials obtained with the use of low energy electron microscopy (LEEM) and photoelectron emission microscopy (PEEM). We address the growth and the locally resolved electronic structure of an organic semiconductor, diindenoperylene, deposited on Au(100) and Au(111) single crystals, taking into account also the lattice geometry of the substrates. In addition, we present the results that we have obtained on a metal-free organic magnet, a derivative of the nitronyl nitroxide, grown on Si(111) surfaces. By taking great advantage of the LEEM and PEEM capabilities, our work has shown that it is possible to deeply understand which parameters influence the XPS spectroscopic lines in phenomena such as photoemission in organic materials. We have also elucidated with the simultaneous investigation of morphology, photoemission and absorption, the existing interplay between morphology, structure and electronic properties. The fact that the different modes of a LEEM–PEEM can be used to comprehensively investigate thin films in situ gives further relevance to the use of these microscopies, when describing fundamental chemical and physical phenomena at the interface and surface of materials.