Mycotoxins present in cereals are a worldwide problem and are a result of the presence of mycotoxin producing fungi. A strategy to reduce these fungi and mycotoxin levels in contaminated grains is with the use of lactic acid bacteria (LAB) or Bacillus spp., which can degrade or bind toxins. In this study, LAB and Bacillus spp. were isolated from mycotoxin contaminated wheat grains and, together with additional plant-derived strains, an antifungal screening against Fusarium graminearum was performed. Furthermore, these strains were screened for their ability to reduce zearalenone (ZEA) and deoxynivalenol (DON). Finally, the mode of action of the most promising microorganisms was investigated by analyzing toxin reduction with viable and dead cells, cell extracts and supernatants. Out of 212 tested strains, 70 showed high antifungal activity and 42 exhibited the ability to detoxify more than 90% ZEA, i.e., Bacillus licheniformis (19), B. megaterium (13), and Levilactobacillus brevis (10). None of the tested strains were able to decrease DON. The mode of action of ZEA reduction could not be fully elucidated. Neither dead cells (<20%), nor cell extracts nor supernatants could reduce ZEA in high amounts, which exclude high binding capacity and the involvement of extra- or intra-cellular enzymes.