While the superconductor proximity effect is well understood in layered superconductor/normalmetal junctions, its understanding is quite limited in systems involving nanoparticles (NPs) and molecules. In recent studies, a unique inverse proximity effect phenomenon was found in which the critical temperatures of Nb films surprisingly increased upon the chemical attachment of gold NPs. Concomitantly, the tunneling density of states on and around the gold NPs was significantly modified, showing either zero-bias peaks or the development of proximity gaps in the NPs. These results seem to be related to the molecule-mediated coupling strength. Here, we study the strong molecular coupling regime of such an architecture, for which proximity gaps are induced in Au NPs. We show that significant pinning is induced in a periodic array of Au NPs coupled to a superconducting surface via organic molecules. The pinning potential in this case is stronger than the potential achieved through the direct proximity of Au or Ni islands to the superconducting surface. A matching field magnetoresistance signal can only be identified using the hybrid Au/organic-linker/Nb system. In this case, the matching vortex lattice density is higher than the saturation number. These results suggest that the NP-Nb electrical coupling through the molecules induces a resonance behavior, which modifies the local pairing amplitude.Superconductivity is a condensation phenomenon involving electronic pairs. As such, superconductivity involves two imperatives: the binding of electrons into pairs and the establishment of phase coherence between the pairs. Phase coherence can also occur between adjacent layers via a mechanism reminiscent of the superconductor (SC) proximity effect (PE). In 1976, Ginzburg [1, 2] proposed the use of layered metal-organicmetal hybrids to explore the possibility of increasing the critical temperature, T C , by the 'exciton mechanism'. The excitonic mechanism in hybrid systems has been studied theoretically by various authors, who have suggested similar geometries to ours (see below) [3]. Although the formation of bound excitons for pairing is not essential, and it is electron-hole interactions that are ultimately involved, the 'excitonic mechanism' label has remained for this area of study. Often, the basic model of pairing forces is based on a total dielectric function approach, and some researchers claim that no coupling is possible [4]. These problems with the formalism seem to arise due to the neglect of local field effects [5]. Recently, using a hybrid superconductor-molecule-NP geometry, it was shown that nanostructured components inherently have local fields that permit coupling, which are lacking in the more conventional metal-semiconductor geometries [6]. This nanostructured geometry provides an opportunity for new types of interactions. In a recent study of such a system, two experimentally unique PE-related phenomena were found, in which T C and the critical current of a Nb film increased upon chemically linking gold NPs...