Fusarium graminearum is a plant-pathogenic fungus that causes the devastating disease “Fusarium head blight” (FHB) in cereal crops such as wheat (Triticum aestivum). It also contaminates grains with mycotoxins, including deoxynivalenol (DON), which turn toxic to humans and animals. This fungus overwinters in crop residues left in the field. The fate of mycotoxins in these crop residues in the soil and their ecological role are still unexplored. Therefore, our objective was to assess whether mycotoxins are maintained in the soil, impact the soil biome and benefit the survival of F. graminearum. A six-month study in microcosms was performed to examine the fate of DON in F. graminearum-contaminated wheat straw and soil, and its impact on soil communities. DON was extracted from straw and soil mixtures, and quantified by high-performance liquid chromatography (HPLC). Fusarium graminearum and total fungal and bacterial molecular biomasses were quantified using real-time polymerase chain reaction (Q-PCR). Nematode and earthworm densities were quantified through binocular observations. Changes in the genetic structure of fungi, bacteria, protozoa, and nematodes communities were determined by terminal restriction fragment length polymorphism (T-RFLP) analyses. Results revealed that DON disappeared from the straw and the soil over time. The rate of disappearance was accelerated when straw was incorporated into the soil and when microcosms contained earthworms. Fungal and bacterial biomass, first stimulated during the incorporation of straw, decreased after 2 weeks and until the end of the experiment (24 weeks). It decreased more strongly in the presence of DON. This negative impact of DON was temporary and at the end of the experiment, the bacterial and fungal biomass was higher in the treatments that received DON than in the other treatments while the population of F. graminearum was unaffected. Similarly, DON modified the community structures of fungi, bacteria and protozoa to various extents but not that of nematodes. DON-contaminated straw was found attractive for earthworms, and its presence stimulated their reproduction or cocoon hatching. The major conclusion is that DON briefly affected soil communities, disappeared over time and gave no observable advantage to soil-borne F. graminearum populations.