This work reports the formation of nanoflowers after annealing of Au/Ni bilayers deposited on SiO2/Si substrates. The cores of the nanoflowers consist of segregated Ni silicide and Au parts and are surrounded by SiOx branches. The SiO2 decomposition is activated at 1050 °C in a reducing atmosphere, and it can be enhanced more by Au compared to Ni. SiO gas from the decomposition of SiO2 and the active oxidation of Si is the source of Si for the growth of the SiOx branches of the nanoflowers. The concentration of SiO gas around the decomposition cavities is inhomogeneously distributed. Closer to the cavity border, the concentration of the Si sources is higher, and SiOx branches grow faster. Hence, nanoflowers present shorter and shorter branches as they are getting away from the border. However, such inhomogeneous SiO gas concentration is weakened in the sample with the highest Au concentration due to the strong ability of Au to enhance SiO2 decomposition, and nanoflowers with less difference in their branches can be observed across the whole sample.