We determined the toxicity of various chlorophenols, especially pentachlorophenol (PCP), on five bacterial strains and studied PCP biodegradation in soils amended with an organomineral complex (OMC) prepared from humic acids (organic part) bound on zeolite (inorganic part). Both components of OMC have excellent sorption properties and are of natural origin and therefore suitable to be used in the environment. Toxicity of chlorophenols depends not only on the number of chlorine atoms but also on their position on aromatic ring, and is thus regiospecific. Biodegradation of PCP was studied in three real completely characterized soil samples, Chernozem, Fluvisol, and Regosol, with and without the addition of OMC. The soils were sterilized and bioaugmented with the bacterial isolate Comamonas testosteroni CCM 7530. The immobilization effect of OMC in relation to PCP depends on the concentration of humic acids (HAs), the PCP concentration, and the content of organic carbon in soil. The microbial activity and the simulated action of acid rains led to the gradual release and biodegradation of the reversibly bound PCP without no initial toxic effect on indigenous or bioaugmented microorganisms. OMC appeared to be a good trap for PCP with potential applications in remediation technology because it reduces the potential toxicity of PCP to microbial community by lowering its bioavailability and thus facilitates its biodegradation.