The abundance of organic waste generated from agro-industrial processes throughout the world has become an environmental concern that requires immediate action in order to make the global economy sustainable and circular. Great attention has been paid to convert such nutrient-rich organic waste into useful materials for sustainable agricultural practices. Instead of being an environmental hazard, biodegradable organic waste represents a promising resource for the production of high value-added products such as bioenergy, biofertilizers, and biopolymers. The ability of some hyperthermophilic bacteria, e.g., the genera Thermotoga and Pseudothermotoga, to anaerobically ferment waste with the concomitant formation of bioproducts has generated great interest in the waste management sector. These biotechnologically significant bacteria possess a complementary set of thermostable enzymes to degrade complex sugars, with high production rates of biohydrogen gas and organic molecules such as acetate and lactate. Their high growth temperatures allow not only lower contamination risks but also improve substrate solubilization. This review highlights the promises and challenges related to using Thermotoga and Pseudothermotoga spp. as sustainable systems to convert a wide range of biodegradable organic waste into high value-added products.