A robust analytical method is required for the determination of low-molecular weight organic acids, which are potential causes of refinery and internal combustion engine corrosion. The ion chromatographic method developed in this study allows the determination of acetic acid and formic acid in diesel oil mixtures with a motor oil volume fraction of up to 10%. The hydrophobic matrix is automatically removed in-line through a matrix elution step with organic solvent and nonaqueous anion-exchange analyte extraction. Acetic acid and formic acid, as the smallest and most acidic aliphatic naphthenic acids, were determined. Gradient anion-exchange chromatography on high-capacity columns in combination with suppressed conductivity detection allowed their selective and sensitive determination. Typical recovery values were from 82 to 107% for each acid in the matrices evaluated with reproducibility less than 5% for acid fortified samples.