Microbial Community Engineering (MCE) is an emerging paradigm in biotechnology, which focuses the attention on microbial consortia or communities, sometimes addressed as microbiomes. Microbial communities are ubiquitous in nature and useful in many areas. Earth’s microbial ecosystems are important in the production of foods, nitrogen fixation and carbon cycles, recycling of micronutrients, bioremediation and in maintaining the health of humans, animals, and plants, among many others. MCE is a growing field that can be exploited to produce bulk and fine chemicals, bioenergy as well as pharmaceuticals by enhancing the effect of natural microbiomes. Adapted/selected microbial consortia have the potential to advance specialized tasks by resorting to high-order communities’ mechanisms, which are difficult to accomplish with monocultures. Notwithstanding the interest in MCE, biotechnological applications remain rudimentary; mixed cultures of partially known composition govern the processes of wastewater treatment and the anaerobic digestion of organic refuses, yet the vast potential of “microbial ecological power”, observed in most natural environments, remains largely underemployed. After a brief overview of key mechanisms that govern microbiomes, this work is aimed to suggest experimental approaches for the separation of constituents of complex microbiomes and to use MCE to reproduce the natural biological order by designing interlinked modular bioreactors where MCE would overcome limitations of natural systems.