Surface patterning using plasmonic nanoparticles has attracted increasing interest owing to their wide use in sensing, imaging and medical applications. In this report we demonstrate bottom-up engineering of size distribution of gold nanoparticles (AuNPs) by dewetting a thin Au film deposited on a single crystal diamond (SCD) substrate with self-organized surface structures induced by ion beam etching (IBE). 14 angstrom of gold was sputtered and dewetted on SCD substrates with and without self-organized nano-patterns. AuNPs on structured substrates are smaller and show narrower size distribution (9.11 +/- 2.17 nm, compared to a reference sample being 9.96 +/- 2.94 nm). The center wavelength of the extinction is red-shifted to 584 nm compared to 574 nm for AuNPs on a smooth surface.