A reliable and inexpensive method for the measurement of proteinogenic amino acids was developed. It allows the screening of large sample volumes that is important for current food and feed applications, but also for future biobased applications. The method is based on acid hydrolysis and automated pre-column derivatision in the injection needle of the autosampler using o-phthalaldehyde/ethanethiol reagent in combination with 9-fluorenylmethyl chloroformate. The calculated mean limit of detection and limit of quantification of pure amino acids were 2.3 and 4.6 µM, respectively. With this method, it was possible to accurately analyse the amino acid composition of bovine serum albumin, soy meal, Jatropha press cake, and cyanophycin. Mean reproducibility of all amino acids from bovine serum albumin was 6.8 %, with a mean recovery of 95 %. The sample run time is 16 min with a total cycle time from injection to injection of an acid hydrolyzed sample of 22 min, resulting in a greener method due to a reduction in solvent consumption.