In this work, we report the formation and growth mechanisms of gold nanoparticles (AuNPs) in eco-friendly deep eutectic solvents (DES; choline chloride and urea). AuNPs are synthesized on the DES surface via a low-energy sputter deposition method. Detailed small angle X-ray scattering (SAXS), UV-Vis, and cryogenic transmission electron microscopy (cryo-TEM) investigations show the formation of AuNPs of 5 nm diameter. Data analysis reveals that for a prolonged gold-sputtering time there is no change in the size of the particles. Only the concentration of AuNPs increases linearly in time. More surprisingly, the self-assembly of AuNPs into a first and second shell ordered system is observed directly by in situ SAXS for prolonged gold-sputtering times. The self-assembly mechanism is explained by the templating nature of DES combined with the equilibrium between specific physical interaction forces between the AuNPs. A disulfide-based stabilizer, bis((2-mercaptoethyl)trimethylammonium) disulfide dichloride, was applied to suppress the self-assembly. Moreover, the stabilizer even reverses the self-assembled or agglomerated AuNPs back to stable 5 nm individual particles as directly evidenced by UV-Vis. The template behavior of DES is compared to that of nontemplating solvent castor oil. Our results will also pave the way to understand and control the self-assembly of metallic and bimetallic nanoparticles.