In low-energy electron microscopy (LEEM) we commonly encounter images which, beside amplitude contrast, also show signatures of phase contrast. The images are usually interpreted by following the evolution of the contrast during the experiment, and assigning gray levels to morphological changes. Through reconstruction of the exit wave, two aspects of LEEM can be addressed: (1) the resolution can be improved by exploiting the full information limit of the microscope and (2) electron phase shifts which contribute to the image contrast can be extracted. In this article, linear exit wave reconstruction from a through-focal series of LEEM images is demonstrated. As a model system we utilize a heteromolecular monolayer consisting of the organic molecules 3,4,9,10-perylene tetracarboxylic dianhydride and Cu-II-Phthalocyanine, adsorbed on a Ag(111) surface.