Metal-assisted chemical etching is useful and cost-efficient for nanostructuring the surface of crystalline silicon solar cells. We have found that the nanoscale epitaxy of silicon occurs, upon subsequent annealing, at the Al₂O₃/Si interface amorphized by metal-assisted etching. Since this epitaxial growth penetrates into the pre-formed Al₂O₃ film, the bonding nature at the newly formed interfaces (by the regrown epitaxy) is deteriorated, resulting in a poor performance of Al₂O₃ passivation. Compared to the conventional hydrogen (H–) passivation, hydroxyl functionalization by oxygen plasma treatment was more effective as the wafer became thinner. For ultrathin (∼50 μm) wafers, ∼30% depression in surface recombination velocity led to the improvement of ∼15.6% in the short circuit current. The effectiveness of hydroxyl passivation validated by ultrathin wafers would be beneficial for further reducing the wafer cost of nanostructured silicon solar cells.