The α-phase waveguides directly produced in one fabrication step only are well known for preserving both the excellent nonlinear properties and the ferroelectric domains orientation of lithium niobate substrates. However, by using the piezoresponse force microscopy (PFM), we present a coherent study on ferroelectric dipoles switching induced by the fabrication process of α-phase waveguides on Z-cut congruent lithium niobate (CLN) substrates. The obtained results show that the proton exchange process induces a spontaneous polarization reversal and a reduction in the piezoelectric coefficient d33. The quantitative assessments of the impact of proton exchange on the piezoelectric coefficient d33 have been quantified for different fabrication parameters. By coupling systematic PFM investigation and optical characterizations of α-phase protonated regions and virgin CLN on ±Z surfaces of the samples, we find a very good agreement between index contrast (optical investigation) and d33 reduction (PFM investigations). We clearly show that the increase in the in-diffused proton concentration (increase in index contrast) in protonated zones decreases the piezoelectric coefficient d33 values. Furthermore, having a high interest in nonlinear performances of photonics devices based on PPLN substrates, we have also investigated how deep the spontaneous polarization reversal induced by proton exchange takes place inside the α-phase channel waveguides.