The adsorption of molecules on surfaces affects the surface dipole and thus changes in the work function may be expected. The effect in change of work function is particularly strong if charge between substrate and adsorbate is involved. Here we report the deposition of a strong electron acceptor molecule, tetrafluorotetracyanoquinodimethane C12F4N4 (F4TCNQ) on a monolayer of hexagonal boron nitride nanomesh (h- BN on Rh(111)). The work function of the F4TCNQ/h-BN/Rh system increases upon increasing molecular coverage. The magnitude of the effect indicates electron transfer from the substrate to the F4TCNQ molecules. Density functional theory calculations confirm the work function shift and predict doubly-charged F4TCNQ2− in the nanomesh pores, where the h-BN is closest to the Rh substrate, and to have the largest binding energy there. The preferred adsorption in the pores is conjectured from a series of ultraviolet photoelectron spectroscopy data, where the σ bands in the pores are first attenuated. Scanning tunneling microscopy measurements indicate that F4TCNQ molecules on the nanomesh are mobile at room temperature, as “hopping” between neighboring pores is observed.