Atomic hydrogen is commonly used to clean GaAs surfaces. The goals of this work are to optimize the cleaning process and to control surface reactions in order to avoid decomposition of GaAs. Chemically polished GaAs (001) surfaces have been cleaned by thermally generated atomic hydrogen and analyzed by surface sensitive techniques. We propose an optimal process involving two exposures. The first one at room temperature etches As oxides. The second one at 300 °C completes the reduction of Ga oxides. We demonstrate that the variations of the ionization energy, work function, and Fermi level are very sensitive to the completion of the cleaning reaction. These parameters can be used to monitor surface reactions on‐line in order to avoid excessive desorption of As and GaAs decomposition.