The influence of the annealing atmosphere on the temperature induced phase separation of Ge oxide in GeO(x)/SiO(2) multilayers (x≈1), leading to size controlled growth of Ge nanocrystals, is explored by means of x-ray absorption spectroscopy at the Ge K-edge. Ge sub-oxides contained in the as-deposited multilayers diminish with increasing annealing temperature, showing complete phase separation at approximately 450 °C using inert N(2) ambient. The use of reducing H(2) in the annealing atmosphere influences the phase separation even at an early stage of the disproportionation. In particular, the temperature regime where the phase separation occurs is lowered by at least 50 °C. At temperatures above 400 °C the sublayer composition, and thus the density of the Ge nanocrystals, can be altered by making use of the reduction of GeO(2) by H(2).