This work investigates the effect of gold nanoparticle (AuNP) addition to paper substrate and examines the ability of these composite materials to amplify the surface enhanced Raman scattering (SERS) signal of a dye adsorbed. Paper has a three-dimensional (3D), porous, and heterogeneous morphology. The manner in which paper adsorbs the nanoparticles is crucial to its SERS properties, particularly with regards to aggregation. In this work, we sought to maintain the same degree of aggregation, while changing the concentration of nanoparticles deposited on paper. We achieved this by dipping paper into AuNP solutions of different, known concentration and found that the initial packing density of AuNPs in solutions was retained on paper with the same degree of aggregation. The surface coverage of AuNPs on paper was found to scale linearly to their concentration profile in solutions. The SERS performances of the AuNP-treated papers were evaluated with 4-aminothiophenol (4-ATP) as the Raman molecule, and their SERS intensities increased linearly with the AuNPs' concentration. Compared to AuNP-treated silicon, the Raman enhancement factor (EF) from paper was relatively higher due to a more uniform and greater degree of adsorption of AuNPs. The effect of the spatial distribution of AuNPs in their substrates on SERS activity was also investigated. In this experiment, the number of AuNPs was kept constant (a 1 μL droplet of AuNPs was deposited on all substrates), and the distribution profile of AuNPs was controlled by the nature of the substrate: paper, silicon, and hydrophobized paper. The AuNP droplet on paper showed the most reproducible and sensitive SERS signal. This highlighted the role of the z-distribution (through film) of AuNPs within the bulk of the paper, producing a 3D multilayer structure to allow inter- and intralayer plasmon coupling, and hence amplifying the SERS signal. The SERS performance of nanoparticle-functionalized paper can thus be optimized by controlling the 3D distribution of the metallic nanoparticles, and such control is critical if these systems are to be implemented as a low-cost and highly sensitive bioassay platform.