Methods and systems are presented for heterogeneous integration of photonics and electronics with atomic layer deposition (ALD) bonding. One method includes operations for forming a compound semiconductor and for depositing (e.g., via atomic layer deposition) a continuous film of a protection material (e.g., Al2O3) on a first surface of the compound semiconductor. Further, the method includes an operation for forming a silicon on insulator (SOI) wafer, with the SOI wafer comprising one or more waveguides. The method further includes bonding the compound semiconductor at the first surface to the SOI wafer to form a bonded structure and processing the bonded structure. The protection material protects the compound semiconductor from acid etchants during further processing of the bonded structure.