Microbial community engineering (MCE) is a growing branch of the biotechnological field, which uses co-cultures or mixed cultures of different strains or species to exploit the natural diversity and interactions among microbial groups. Urgent concerns regarding the Water-Energy-Food-Waste (WEFW) nexus started to raise a couple of years ago, while biological systems have long addressed the nexus issues for their survival since ancient times. The availability of carbon (food/waste) and energy sources (solar or chemical), as well as water activity in specific environments, has shaped through evolution the metabolism of individual and mixed consortia of microorganisms. The accumulation of metabolic products or the depletion of substrates in a given natural niche can potentially modify the environmental conditions and hence promote population selection shifts. Microbial consortia present species–species and species–environment interactions, which can exert selective pressure and influence the complex interplay of the biological system. Microbial communities sustain a range of ecosystem services, including freshwater supply, carbon and nitrogen cycles, human health, bioenergy production, CO2 sequestration and bioremediation. The present review addresses higher-order properties of microbial communities, such as interspecies electron transfer and quorum sensing, highlighting some of the available applications and tools of MCE in the context of the WEFW nexus.