In this work, we investigated the effect of plasma-chemical treatment of silicon substrates on the subsequent epitaxial growth of GaAs. It is shown that a change in processing modes did not lead to a strong change in the root-mean-square roughness of the initial silicon surface. It was found that under the same growth conditions GaAs is formed on substrates differently depending on the silicon treatment mode: from individual crystallites with nanowires to a structure intergrown from individual crystallites. It is shown that a change in the annealing temperature significantly affects the resulting surface morphology.