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Optically transparent, electrically conductive n-Si/n-GaAs direct wafer bonds are achieved by a thorough optimization of surface conditioning using fast atom beams. Bonding at room temperature under high-vacuum conditions is systematically investigated after in situ surface deoxidization using either argon or helium fast atom beams. Using argon, high bond energies of up to 900 mJ/m2 are obtained and further enhanced to achieve bulk strength through rapid annealing at 290 °C, thereby enabling the production of thermally stable and mechanically robust hybrid substrates. Moreover, the interface conductivity is significantly improved by an additional thermal annealing at 400 °C. Although it is anticipated to induce higher quality interfaces, helium treatment yields, however, limited and unstable bonding. This difference is attributed to an important surface nano-texturing that occurs during fast atom beam processing, a phenomenon that is peculiar to helium and absent in argon treatment.