Aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM) has enabled atomically resolved imaging of molecules adsorbed on low-dimensional materials like carbon nanotubes, graphene oxide and few-layer-graphene. However, conventional methods for depositing molecules onto such supports lack selectivity and specificity. Here, we describe the chemically selective preparation and deposition of molecules-like polyoxometalate (POM) anions [PWO] using electrospray ion-beam deposition (ES-IBD) along with high-resolution TEM imaging. This approach provides access to sub-monolayer coatings of intact molecules on freestanding graphene, which enables their atomically resolved ex situ characterization by low-voltage AC-HRTEM. The capability to tune the deposition parameters in either soft or reactive landing mode, combined with the well-defined high-vacuum deposition conditions, renders the ES-IBD based method advantageous over alternative methods such as drop-casting. Furthermore, it might be expanded towards depositing and imaging large and nonvolatile molecules with complex structures.