The present invention is a modular bio-digestion system wherein each module within the system includes at least one stage in the bio-digestion process. Modules can be arranged in a variety of configurations. At least some of the operational parameters of the system are optimizable and include at least one of operational temperature for each stage of the overall system contained within that module, and/or the pH, and/or the microbe population and mixture, and/or the gas composition, and/or the quantity of applicable additives or reagents, used by that particular stage of the system, contained within the module, and wherein each module within the system is contained within a standard 20 or 40 foot shipping container. N-I 0) C')