Laser-induced structuring of nanoporous glass composites is promising for numerous emerging applications in photonics, plasmonics, and medicine. In these laser interactions, an interplay of photo-thermo-chemical mechanisms is commonly activated and is extremely difficult to control. The choice of optimum laser parameters to tune the resulted optical properties remains extremely challenging. In this paper, we analyze the mechanisms involved and propose a way to control not only structures formed by laser inside nanoporous glass composites doped by metallic ions and nanoparticles, but also their plasmonic properties. For this, both experimental and numerical approaches are combined. The transmitted and reflected laser powers are used to analyze the modification process. Spectral microanalysis provides plasmonic properties. Numerical effective medium modeling connects the measured data to the estimated size, concentration, and chemical composition of the second phase across the initial sample.