We have modeled the decomposition of nonstoichiometric amorphous SiOx upon annealing into silicon and stoichiometric silica, using a new method based on mapping Metropolis Monte Carlo simulations onto rate equations. The concentrations of all oxidation states of silicon are derived as a function of time and found to attain steady-state values at long times dependent on temperature T and oxygen content x. The degree of phase separation and the sizes of Si particles are predicted as a function of T and x, enabling greater control over the size of silicon quantum dots in silica matrices.