Environmental processes can affect the stereochemical properties of organic pollutants. In particular, biotic processes like microbial transformations or membrane penetration alter the ratios of enantiomers as well as diastereomers. These effects have been intensively used not only in environmental studies but also in medicine, toxicology, pharmacy, and agricultural sciences. However, in order to identify unambiguously biotic-initiated alteration of organic compounds, the knowledge on the stereoselective effect of all relevant processes is mandatory. Therefore, here we report the first evidence for a stereospecific formation of non-extractable residues of a xeniobiotic in a highly relevant soil subfraction, the organo-clay complexes. In this study, soils were spiked with labeled and unlabeled nonylphenol isomer, and incubation experiments were performed to study its long-term incorporation behavior into soil-derived organo-clay complexes under abiotic and biotic conditions. Besides the extractable particle-associated proportion especially the humic fractions comprising the bound residues have been analyzed by GC/ MS. Our results from biotic experiments revealed alterations of the diastereomeric composition of the contaminant in the different soil humic subfractions. A depletion of the first eluting diastereomer as expressed by diastereomeric ratios around 0.6 has been observed for the extractable fraction, whereas the non-extractable proportion was enriched in the first diastereomer (diasteremoric ratio around 1.0). On the contrary, the diastereomeric ratios remained unaffected during the abiotic experiments (diasteremoric ratio around 0.8). These systematic observations give clear evidence that the process of microbial-assisted incorporation of nonylphenol into soil organo-clay complexes is a stereoselective process. To our knowledge, this is the first report on a stereoselective incorporation process of organic substances forming non-extractable residues. Consequently, the formation of non-extractable residues has to be considered in environmental studies dealing with stereoselective analysis of organic pollutants in soils to study their microbial transformation.