Predicting the fate of engineered nanoparticles (ENPs) once they are released in the environment is essential to evaluate their impacts to ecosystems. Microbial biofilms, as highly reactive compartments in soils and sediments, have the potential to impose strong controls on ENPs life cycle in natural settings. However, information regarding impacts of biofilms toward ENPs environmental fate are not easily accessible, and such evidences are collected and discussed in this review, in order to identify common trends and to better constrain the role played by these microbial structures. Biofilms are reported to exhibit important ENPs accumulation capacities, and short to long-term ENPs immobilization can thus be expected. Mechanisms that govern such accumulation and ENPs migration within biofilms depend strongly on electrostatic and hydrophobic interactions, as well as biofilm structural properties, such as density and permeability. They are a combination of key parameters that include ENPs size and surface properties, mineral substrate reactivity, ability to develop organic corona around ENPs, or formation of aggregates within the biofilm thickness. In addition, these microbial structures exhibit highly reactive microenvironments, and are consequently able to impose major ENPs transformations such as dissolution, through ligand- or redox-mediated pathways, as well as passivation or stabilization processes. Interestingly, exposure to toxic ENPs can even trigger a response from micro-organisms biofilms which has the potential to strongly modify ENPs speciation. Promising approaches to investigate the role of microbial biofilms for ENPs cycling in realistic systems are introduced through the use of mesocosms, medium-size replicated ecosystems that allow to integrate the complexity of natural settings. Finally, biofilm-mediated nanoparticles synthesis in man-impacted systems is presented. This raises important questions regarding biofilms role as secondary sources of nanoparticles.