Background High doses of ethylenebisdithiocarbamate (EBDC) are used in banana production, and unused pesticide mixture (solution) is often disposed of improperly. This can result in soil and water contamination and present an undue risk to rural communities and the environment. An alternative to reduce the environmental impacts caused by pesticide residues is the biobeds treatment. It is necessary to establish if the composition of the proposed biomixtures supports microbial activity to degrade pesticides in biobeds. This research aimed to evaluate the EBDC effect on the distribution and abundance of microbial populations in polluted biomixtures . Methods For this purpose, a biomixture based on banana stem, mulch, and Fluvisol soil (50:25:25% v/v) was prepared and polluted with 1,000 mg L.sup.-1 EBDC. The response variables kinetics were determined every 14 days for three months, such as pH, organic matter, moisture, cation exchange capacity, microbial colonies, and cell counts at three depths within the experimental units. Results EBDC reduced the number of microbial colonies by 72%. Bacterial cells rapidly decreased by 69% and fungi 89% on the surface, while the decrease was gradual and steady at the middle and bottom of the biobed. The microbial populations stabilized at day 42, and the bacteria showed a total recovery on day 84, but the fungi slightly less. At the end of the experiment, the concentration of EBDC in the biomixture was 1.3-4.1mg L.sup.-1 . A correlation was found between fungal count (colonies and cells) with EBDC concentration. A replacement of the biomixture is suggested if the bacterial population becomes less than 40x10.sup.6 CFU mL.sup.-1 and the fungal population less than 8x10.sup.4 CFUmL.sup.-1 or if the direct cell count becomes lower than 50x10.sup.4 cells mL.sup.-1 in bacteria and 8x10.sup.2 cells mL.sup.-1 in fungi. Conclusion The biomixture based on banana stem supports the microbial activity necessary for the degradation of the EBDC pesticide. It was found that fungi could be used as indicators of the pollutant degradation process in the biomixtures. Microbial counts were useful to establish the mobility and degradation time of the pesticide and the effectiveness of the biomixture. Based on the results, it is appropriate to include the quantification of microbial populations to assess the effectiveness of pesticide degradation and the maturity level of the biomixture.