Transparent alumino(boro)silicate glasses containing tin-doped indium oxide nanocrystals were fabricated using conventional melt-casting and heat treatment. Structural characterization was carried out by Raman spectroscopy to study glass-forming species, coordination, type and number of oxygens, and possible connectivity of silicate, aluminate, and borate species. A changing role of indium, acting as a modifier in the glass structure, but leaving a less modified glass after clustering and crystallization was also revealed. X-ray photoelectron spectroscopy confirmed that indium was in the trivalent state only. HR-TEM provided insights into the distribution and morphology of the nanocrystals in the glass ceramic sample, yielding a mean size of 4.75 nm. The nonlinear optical behavior of aluminoborosilicate glass samples was evaluated using the Z-scan technique, demonstrating high third-order nonlinear optical susceptibility for both glass and glass ceramic samples, accompanied by a change in the signs of nonlinear refractive indices before and after crystallization from negative to positive.