Integrating biofuels with conventional petroleum products requires improvements in processing to increase blendability with existing fuels. This work demonstrates analysis techniques for more hydrophilic bio-oil liquids that give improved quantitative and qualitative description of the total acid content and organic acid profiles. To protect infrastructure from damage and reduce the cost associated with upgrading, accurate determination of acid content and representative chemical compound analysis are central imperatives to assessing both the corrosivity and the progress toward removing oxygen and acidity in processed biomass liquids. Established techniques form an ample basis for bio-liquids evaluation. However, early in the upgrading process, the unique physical phases and varied hydrophilicity of many pyrolysis liquids can render analytical methods originally designed for use in petroleum-derived oils inadequate. In this work, the water solubility of the organic acids present in bio-oils is exploited in a novel extraction and titration technique followed by analysis on the water-based capillary electrophoresis (CE) platform. The modification of ASTM D664, the standard for Total Acid Number (TAN), to include aqueous carrier solvents improves the utility of that approach for quantifying acid content in hydrophilic bio-oils. Termed AMTAN (modified Total Acid Number), this technique offers 1.2% relative standard deviation and dynamic range comparable to the conventional ASTM method. Furthermore, the results of corrosion product evaluations using several different sources of real bio-oil are discussed in the context of the unique AMTAN and CE analytical approaches developed to facilitate those measurements.