Graphene-based materials (GBMs) are gaining more and more attention from the scientific community due to their unique properties. One of the major concerns is to deliver the safest material possible on the market. To address this challenge, assessing the GBM ecotoxicity is required. Microbial communities are present in every environmental compartment, are at the basis of every trophic chain and endorse many essential roles in the environment and in engineered systems such as element cycling. Studies conducted on GBMs' impact mainly focused on the effect of GBMs towards mono species cultures of bacteria and algae, which are not environmentally relevant. This review examines recent advances about GBM effects on complex microbial communities, bringing together ecotoxicology and bioprocess engineering research, two major and complementary fields in environmental sciences. This review reveals the potential of GBMs to disrupt the growth of the communities but also their structure and diversity in a broad spectrum of environmental conditions. Multiple studies reported the disruption of carbon and nitrogen cycling throughout the perturbation of related species. Electron transfer, on which relies many bioprocesses, was also found to be enhanced. The fate of antibiotic resistance genes was also influenced. Moreover, communities seemed to exhibit a form of resilience through composition modifications and also by reducing the oxidation state of the GBMs. Nevertheless, GBMs are pointed out as disruptors of the structure and activity of microbial communities, which could lead to larger environmental consequences as these communities are at the basis of every ecosystem's health.