The economics of biodiversity is gaining traction and with it the economic valuation of ecosystem services (ESS). Most current developments neglect microbial diversity, although microbial communities provide ecosystem services of great importance. Here we argue that microbial biodiversity (hereafter microbiodiversity) translates into considerable economic value which is usually not explicitly included in quantitative valuation of ecological functions to date. This omission may result in inaccurate values, potentially entailing substantial economic losses, both in private and in public decision-making, due to external effects that arise as microbiodiversity is horizontally and vertically transferred between hosts and natural environments. Microbiodiversity, an important part of biodiversity in general, occupies an irreplaceable position as a natural resource in ecosystems, because of option values derived from the evolutionary potential of microbes, especially if host-associated, and also because of their additional insurance value within changing environments. We illustrate our arguments with specific examples (microbiomes associated with humans, soil, and corals), all of which are jeopardized through anthropogenic pressure. We conclude that the consideration of microbiodiversity in economic valuation will help to find essential assets and guide decision-makers to conserve and protect the economic value of highly diverse microbial communities for future generations.