Quality and process control of biofuels require straightforward, fast and accurate analysis methods. Ion chromatography (IC) is at the leading edge of this effort. Traces of anions in a gasoline/ethanol blend can accurately be determined in the sub-ppb range after Metrohm Inline Matrix Elimination using anion chromatography with conductivity detection after sequential suppression. While the analyte anions are retained on the preconcentration column, the interfering organic gasoline/bioethanol matrix is washed away.Detrimental alkali metals and water-extractable alkaline earth metals in biodiesel are determined in the sub-ppm range using cation chromatography with direct conductivity detection applying automated extraction with nitric acid and subsequent Metrohm Inline Dialysis. Unlike high-molecular substances, ions in the high-ionic strength matrix diffuse through a membrane into the low-ionic water acceptor solution. In biogas reactor samples, low-molecular-weight organic acids stem from the biodegradation of organic matter. Their profile allows important conclusions concerning conversion in the anaerobic digestion reaction. Volatile fatty acids and lactate can be accurately determined by using ion-exclusion chromatography with suppressed conductivity detection after inline dialysis or filtration.