The present study evaluates the ionization efficiency (IE) of linear and branched C2–C14 dicarboxylic acids (DCAs) by electrospray ionization (ESI) under different conditions. The influence of the concentration of organic modifier (MeOH); mobile phase additive; and its concentration, pH, and DCA structure on IE values is studied using flow injection analysis. The IE values of DCAs increase with the increase of MeOH concentration but also decrease with an increase of pH. The former is due to the increase in solvent evaporation rates; the latter is caused by an ion-pairing between the diacid and the cation (ammonium), which is confirmed by the study with different amines. The investigation of DCA ionization in the presence of different acidic mobile phase additives showed that a significant improvement in the (−)ESI responses of analytes was achieved in the presence of weak hydrophobic carboxylic acids, such as butyric or propanoic acid. Conversely, the use of strong carboxylic acids, such as trichloroacetic acid, was found to cause signal suppression. The results of the IE studies were used to develop the liquid chromatography–high-resolution mass spectrometry (LC-HRMS) method that provided instrumental limits of detection in the range from 6 to 180 pg. Furthermore, upon applying the nonparametric Gaussian process, a model for the prediction of IE values was developed, which contains the number of carbons in the molecule and MeOH concentration as model parameters. As a case study, dicarboxylic acids are quantified in salt-rich effluent and blood serum samples using the developed LC-HRMS method.