The modern development of nanotechnology requires the discovery for simple approaches that ensure the controlled formation of functional nanostructures with a predetermined morphology. One of the simplest approach is a self-assembly of nanostructures. The widespread implementation of self-assembly is limited by the complexity of controlled processes in a large volume, where due to the temperature, ion concentration, and other thermodynamics factors, local changes in diffusion-limited processes may occur, leading to unexpected nanostructures growth. Much easiest way to control the diffusion-limited processes is spatial limitation and localized growth of nanostructures in porous matrix. In this paper, we propose to apply the method of controlled self-assembly of gold nanostructures in a limited pore volume of a silicon oxide matrix with submicron pore sizes. A detailed study of achieved gold nanostructures morphology, microstructure, and surface composition at different formation stages is carried out to understand the peculiarities of realized nanostructures. Based on the obtained results, a mechanism for the growth of gold nanostructures in a limited volume, which can be used for the controlled formation of nanostructures with a predetermined geometry and composition have been proposed. The results observed in the present study can be useful for the design of plasmonic-active surfaces for surface enhanced Raman spectroscopy based detection of ultra-low concentration of different chemical or biological analytes, where the size of the localized gold nanostructures is comparable with the spot area of the focused laser beam.