Heterogeneous assemblies of molecules (Rhodamine B) adsorbed onto a nano-corrugated metallic surface (a percolated Au network) are investigated using electron energy loss spectroscopy in the scanning transmission electron microscope (STEM-EELS). Our first measurements target the native metallic substrate, which consists of a commercial Au thin film atop an ultrathin carbon membrane. The Au film displays a percolated morphology with nanostructures of estimated thickness ≤10 nm approximately. We observe a rich plasmonic response from the metallic substrate; one which varies nanometrically and spans the VIS-terahertz region. Multiple localized plasmons are detected at individual nanometric integrated areas, while an analysis of their spatial distribution reveals that for each integrated energy range (50 meV integration window) resonances are simultaneously supported at different locations within the film. We record subsequent EEL spectrum images of the hybrid molecular-metallic construct after deposition of Rhodamine B molecules onto the substrate, where plasmons, molecular vibrations and electronic excitations might all be simultaneously detected. A comparison of average signals for both systems is performed and spectral variations within the three spectral regions where molecular signatures may be observed are discussed. Our measurements and their analysis, if applied to the same location before and after molecular deposition, may be used to rationalize optical microscopic and spectroscopic measurements that take advantage of the interplay between molecules and plasmons.