There is increasing concern about modifications to pesticide persistence in soil from the application of organic wastes as fertilizers. This study was conducted to discriminate the multiple effects of biogas residues (BR) amendment, including soil nutrients, soil microbial activity and biodiversity, and adsorption and degradation of chloroacetanilide herbicides (acetochlor, metolachlor, and butachlor). Addition of BR to soil increased the release of organic materials (i.e., dissolved organic carbon, dissolved organic nitrogen, and active phosphorus). It not only stimulated soil microorganisms and caused changes to microorganism diversity but also increased herbicide adsorption. Such multiple effects led to selective decontamination of chloroacetanilide herbicides, depending on herbicide structures and BR amendment levels. Stereoselectivity in degradation of acetochlor and metolachlor with biphasic character was magnified by BR amendment, which was well explained by integrating the impacts of BR amendment. Interestingly, BR amendment induced significant accumulation of herbicidally active aS,CS-metolachlor, facilitating the utilization of herbicidal activity.