The controlled assembly of plasmonic nanoparticles is vital for realizing low-cost, high efficiency plasmonic substrates with tunable resonances. Here, we present a strategy to assemble gold nanoparticles (AuNPs) in resonant gold nanoapertures (NAs) to enable coupling-mediated near-field enhancement. The NAs templates are fabricated using shadow sphere lithography on polyelectrolyte (PE) coated substrates. Subsequently, AuNPs are assembled in the resonant NA templates via a simple immersion step. The PE layer, AuNP concentration, NaCl concentration, incubation time, and template thickness are used to control the particle number per aperture and the interparticle distance of the AuNP assemblies. The fabricated AuNP-NA substrates are evaluated for their SERS potential using 4-Mercaptobenzoic acid (MBA) as a Raman reporter molecule. The SERS intensity of the AuNP-NA templates can be enhanced by ten times by controlling the AuNP and NA template parameters as compared to the bare NA templates. Numerical simulations show that the coupling between the various plasmonic modes is crucial for this SERS enhancement. The proposed strategy can be used to fabricate hybrid AuNP-NA based SERS substrates with improved sensitivity. © 2022 IOP Publishing Ltd.