Quantification of nonextractable residues (NER) of pesticides in soil is feasible by use of radioactively labeled compounds, but structural information on these long-term stabilized residues is usually lacking. Microorganisms incorporate parts of the radiolabeled ((14)C-) carbon from contaminants into microbial biomass, which after cell death enters soil organic matter, thus forming biogenic nonextractable residues (bioNER). The formation of bioNER is not yet determinable in environmental fate studies due to a lack of methodology. This paper focuses on the development of a feasible analytical method to quantify proteinaceous carbon, since proteins make up the largest mass portion of bacterial cells. The test substance (14)C-bromoxynil after 56 days forms more than 70% of NER in soil. For further characterization of NER the amino acids were extracted, purified, and separated by two-dimensional thin-layer chromatography (TLC). Visualization of the (14)C-amino acids was performed by bioimaging, unambiguous identification by GC-MS and LC-MS/MS. Our analysis revealed that after 56 days of incubation about 14.5% of the (14)C-label of bromoxynil was incorporated in amino acids. Extrapolating this content based on the amount of proteins in the biomass (55%), in total about 26% of the NER is accounted for by bioNER and thus is not environmentally relevant.