Local reactivity on periodically proton exchanged lithium niobate (PPE:LN) surfaces is a promising route for the fabrication of regularly spaced nanostructures. Here, using MgO-doped PPE:LN templates, we investigate the influence of the doping on the nanostructure formation as a function of the proton exchange (PE) depth. The deposition is found to occur preferentially along the boundary between MgO-doped LN and the PE region when the PE depth is at least 1.73 μm, however, for shallower depths, deposition occurs across the entire PE region. The results are found to be consistent with an increased photoconductivity of the MgO-doped LN.