The soil microbiome plays an important role in the establishment of weeds and invasive plants. They associate with microorganisms supporting their growth and health. Weed management strategies, like tillage and herbicide treatments, to control weeds generally alter soil structure going alongside with changes in the microbial community. Once a weed population establishes in the field, the plants build up a close relationship with the available microorganisms. Seeds or vegetative organs overwinter in soil and select early in the season their own microbiome before crop plants start to vegetate. Weed and crop plants compete for light, nutrition and water, but may differently interact with soil microorganisms. The development of new sequencing technologies for analyzing soil microbiomes has opened up the possibility for in depth analysis of the interaction between ‘undesired’ plants and crop plants under different management systems. These findings will help us to understand the functions of microorganisms involved in crop productivity and plant health, weed establishment and weed prevention. Exploitation of the knowledge offers the possibility to search for new biocontrol methods against weeds based on soil and plant-associated microorganisms. This review discusses the recent advances in understanding the functions of microbial communities for weed/invasive plant establishment and shows new ways to use plant-associated microorganisms to control weeds and invasive plants in different land management systems.