In the twenty-first century, scientists will want to steer the microbial black box in (engineered) ecosystems, rather than only study and describe them. This strategy led to a new way of thinking: Microbial Resource Management (MRM). For the last few years, MRM has been utilized to consolidate and communicate our acquired knowledge of the microbiome to many areas of the scientific community. This shared knowledge has brought us closer to formulating a plan toward the analysis, and at a later stage, the management of our varied microbial communities and to look at ways of harnessing their unique abilities for future practices. We require this acquired knowledge for a more sustainable solution to our ongoing global challenges such as our diminishing energy and water supply. Like any successful concept, MRM must be updated to adapt to new molecular technologies, and thus, in this review, MRM has been reengineered to encompass these changes. This review reports how MRM has been used successfully over the last few years within various environments and how we can broaden its capabilities to increase its compliance in the face of state of the art ever changing technologies. Not only have we reengineered and improved MRM, but also we have discussed how newly formed relationships between technologies can provide the full picture of these complex microbial communities and their interactions for future opportunities.