Damage of the hydrogenated amorphous/crystalline silicon interface passivation during transparent conductive oxide sputtering is reported. This occurs in the fabrication process of silicon heterojunction solar cells. We observe that this damage is at least partially caused by luminescence of the sputter plasma. Following low-temperature annealing, the electronic interface properties are recovered. However, the silicon-hydrogen configuration of the amorphous silicon film is permanently changed, as observed from infra-red absorbance spectra. In silicon heterojunction solar cells, although the as-deposited film’s microstructure cannot be restored after sputtering, no significant losses are observed in their open-circuit voltage