Ion-permselective nanochannel-based sample preconcentration or electropreconcentration has been demonstrated as an effective technique for concentrating charged analytes at the interface between a micro- and nanochannel. The anion-selective electropreconcentration involves extraction of hydroxide in the preconcentrated sample plug, resulting in pH decrease. We investigated the pH change in a microchannel using charged pH indicators with different conditions including running buffer pH, sample channel electric field, and salt concentration. The anion-selective preconcentration showed pH decrease from 11 to under 7 in the preconcentrated sample plug. Therefore, careful design and interpretation are required with pH-dependent experiments such as analyzing enzyme or antibody characteristics. The pH change could be mitigated by reducing the sample channel electric field and/or increasing salt concentration in the buffer.