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A microcosm study was conducted at two different temperatures under laboratory conditions to investigate the regulatory capacity and the interactive performance of two soil fauna species (Aporrectodea caliginosa, earthworms, and Proisotoma minuta, collembolans) on the reduction of Fusarium toxins in contaminated maize stubbles. Single and mixed species treatments were exposed to artificially infected maize stubbles highly contaminated with the mycotoxins deoxynivalenol (DON) (10,462 µg kg−1) and zearalenone (ZEN) (2,780 µg kg−1) at 17 °C and 25 °C for time periods of 3 and 6 weeks. Immediately after the respective end of incubation, the microcosms were heavily watered to determine the leaching potential of DON and ZEN from contaminated maize stubbles. Maize residues, soil, and eluted water (percolate) samples were analysed for mycotoxin content using liquid chromatography coupled to mass spectrometry. The biomass of introduced earthworms and number of collembolans were monitored to get information about their adaptability to the experimental conditions. While the decline of ZEN was temperature-dependent, but not influenced by faunal activities, a reduction of DON due to faunal impact was observed by trend. In the leaching experiment, 67–82% of the DON content in the residual maize stubbles leached from the plant material by irrigation and was detected in the soil (1.9–3.4 µg kg−1) and in the percolate (12–295 µg L−1). In the case of ZEN, 27–50% of the mycotoxin leached from the residual maize stubbles due to watering but was only occasionally detected in traces in the soil and not found in the percolate. The results clearly reveal a leaching potential of both DON and ZEN, respectively, but a mobilisation with water was only observed for DON. Temperature confirmed to be a key factor, affecting the fate of the mycotoxins in the soil by driving the interaction between different soil fauna members as well as functional and trophic levels within the soil food web.