Exploiting the potential of bacteria in phytoremediation for the removal of organic and inorganic pollutants from soils and (ground)water holds great promise. Besides bacteria, mycorrhizal fungi and free-living saprotrophs are well known for their strong degradative capacities and plant growth promotion effects, which makes them of high interest for use in different bioremediation strategies. To further increase the efficiency and successes of phytoremediation, interactions between plants and their associated microorganisms, both bacteria and fungi, should be further investigated, in addition to the close interactions between bacteria and fungi. Benefitting from an increased understanding of microbial community structure and assembly allows us to better understand how the holobiont can be modified to improve pollutant degradation and plant growth. In this review, we present an overview of insights in plant-bacteria-fungi interactions and the opportunities of exploiting these tripartite interactions to enhance the effectiveness of phytoremediation of organic pollutants.