The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.

Hydrogen is widely considered as the fuel of the future. Due to the challenges present during hydrogen production using conventional processes and technologies, additional methods must be considered, like the use of microorganisms. One of the most promising technologies is dark fermentation, a process where microorganisms are utilized to produce hydrogen from biomass. The paper provides a comprehensive overview of the biological processes of hydrogen production, specifically emphasizing the dark fermentation process. This kind of fermentation involves bacteria, such as Clostridium and Enterobacterium, to produce hydrogen from organic waste. Synthetic microbial consortia are also discussed for hydrogen production from different types of biomasses, including lignocellulosic biomass, which includes all biomass composed of lignin and (hemi)cellulose, sugar-rich waste waters, and others. The use of genetic engineering to improve the fermentation properties of selected microorganisms is also considered. Finally, the paper covers the important aspect of hydrogen management, including storage, transport, and economics.