In this work we present an innovative method of creating Si quantum dots under pulsed ion-beam exposure. The evolution of defect structure ODC(II) → E'→ ODC(I) → Si QDs in glassy SiO2 under ion-beam implantation was established by optical absorption and photoluminescence spectroscopies. Depending on the mode of ion exposure, it is possible to easily control the type and concentration of defects in the host and modify its optical properties for novel applications. Ab initio calculations confirm that bond softening in SiO2 is attainable via the use of Gd ion implantation. According to our experimental and theoretical results, the three-stage interaction of primary oxygen-deficient centers leads to the formation of stable silicon quantum dots with a size of 3.6 nm and luminescence at 1.8 eV excited by incoherent light.