The controlled tuning of interparticle distance at the nanoscale level is a major challenge for nanofabrication of surface-enhanced Raman scattering (SERS) active clusters and their application to molecular sensing. In fact, the geometrical properties of the narrow gaps between nanoparticles play a key role in determining the local field enhancement (and therefore, the SERS enhancement factor) and the spatial enhancement distribution in the gap region. Besides, very short interparticle distances may block the access of the analyte to the hot zone. In this paper, we report the synthesis of silver colloid NP clusters with interparticle distances fine tuned in the ≤2 nm range, by exploiting the chemical properties of linear α,ω-aliphatic diamines as molecular linkers with varying chain length. The bifunctional diamines also form intermolecular cavities within their self-assembled monolayers, suitable to host molecular analytes for nanosensing applications, as evidenced by SERS detection of organochlorine insecticides at the trace level. In this regard, the extension of the aliphatic chain played a crucial role in determining the SAM conformation and thus the final sensitivity of the functionalized SERS substrate.