Herein we describe how UV excitation of localized electronic states in phosphate glasses can activate structural rearrangements that influence the kinetics of Au nanoparticle (NP) thermal growth in Au-doped glass. The results suggest a novel strategy to address the problem of controlling nano-assembly processes of metal NP patterns in fully inorganic and chemically stable hard materials, such as laser-quality glasses. We show that the mechanism is promoted by opening and subsequent cross-linkage of phosphate chains under UV excitation of non-bridging groups in the amorphous network of the glass, with a consequent modification of Au diffusion and metal NP growth. Importantly, the micro-Raman mapping of the UV-induced modifications demonstrates that the process is restricted within the beam waist region of the focused UV laser beam. This fact is consistent with the need for more than one excitation event, close in time and in space, in order to promote structural cross-linkage and Au diffusion confinement. The stability of the photo-induced modifications makes it possible to design new metal patterning approaches for the fabrication of three-dimensional metal structures in laser-quality materials for high-power nonlinear applications.