Multiphoton photoreduction of photosensitive metallic precursors via direct laser writing (DLW) is a promising technique for the synthesis of metallic structures onto solid substrates at the sub-micron scale. DLW triggered by a two photon absorption process is done using a femtosecond NIR laser (λ = 780 nm), tetrachloroauric acid (HAuCl4) as a gold precursor, and isinglass as a natural hydrogel matrix. The presence of a polymeric, transparent matrix avoids unwanted diffusive processes acting as a network for the metallic nanoparticles. After the writing process, a bath in deionized water removes the gold precursor ions and eliminates the polymer matrix. Different aspects underlying the growth of the gold nanostructures (AuNSs) are here investigated to achieve full control on the size and density of the AuNSs. Writing parameters (laser power, exposure time, and scanning speed) are optimized to control the patterns and the AuNSs size. The influence of a second bath containing Au3+ to further control the size and density of the AuNSs is also investigated, observing that these AuNSs are composed of individual gold nanoparticles (AuNPs) that grow individually. A fine-tuning of these parameters leads to an important improvement of the created structures’ quality, with a fine control on size and density of AuNSs.