The analysis of many environmental and clinical samples requires the modification of the original pH, which is conventionally carried out by manual/automatic addition of acid, base, or buffering reagents. In the case of decentralized measurements, often, this approach is not plausible. Instead, reagentless alternatives, such as electrochemically activated in-situ pH adjustments, are suitable. Herein, we present a method for electrochemical, reversible pH modulation of thin-layer samples (<100 µm thickness) using the co-polymer poly(aniline-co-o-aminophenol) (PANOA). The PANOA's electropolymerization strategy was optimized considering the proton exchange properties in the final material. Thus, limiting the maximum anodic potential to 0.85 V and with the number of cyclic scans being ≤150), the optimal pH modulation capabilities were observed. The reversible proton exchange properties of PANOA were quantified by monitoring the pH inside the thin-layer sample (volume of 0.6 µL), which was defined by a 3D-printed microfluidic cell and a pH-sensor placed in a face planar configuration to the PANOA film. A pH value in the range of 2–4 can repeatably be reached in the samples in 3 min, purely by an electrochemical means and without the addition of external reagents. The concept has been demonstrated to acidify samples at environmental pH (artificial samples and Seawater). The outcomes suggest that the family of polyaniline-co-polymers are interesting to be explored and utilized for electrochemically based pH modulation strategies, if careful considerations are taken regarding their electropolymerization process. Overall, such materials could contribute to the development of continuous, decentralized measuring devices requiring acidification for the formal detection of environmental markers, such as nutrients, carbon species speciation and alkalinity, among others.