Microcystins (MCs), common toxins produced during cyanobacterial blooms, are frequently found in water sources used for irrigation, leading to their introduction into agricultural environments. While MCs are well-known for their toxic effects on plant growth and physiology, their influence on plant-associated microbial communities remains underexplored. To address this gap, we studied how exposure to 100 µg/L of MCs affects the bacterial microbiota inhabiting bulk soil (BS), root-adhering soil (RAS), and root tissue (RT) in Vicia faba using a greenhouse pot experiment. Our findings revealed that MC exposure significantly altered the microbial community structure, co-occurrence patterns, and assembly mechanisms, with the most pronounced changes observed in RT microbiota, followed by BS and then RAS. Notably, MCs caused a marked decline in several Actinobacteriota taxa within RT, particularly members of the genus Streptomyces, which are commonly associated with plant health. In contrast, the abundance of certain Proteobacteria, including Methylobacillus, Methylotenera, and Paucibacter, genera potentially involved in MC degradation, increased under MC treatment. Network analysis showed a reduction in microbial co-occurrence complexity in MC-exposed conditions compared to the control. Moreover, community assembly in RT appeared to be predominantly governed by deterministic processes, while both deterministic and stochastic processes influenced BS and RAS microbiota, with a stronger deterministic trend overall. These results suggest that MCs may reshape the microbiota structure in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with a potential capacity to degrade MCs.