Abstract: The present invention comprises methods and systems for treating biomass wastes to result in usable byproducts. Biomass is treated to remove debris, transferred to microbial digester units, such as anaerobic and aerobic digesters, and the resultant solids and liquids are provided to an algae production unit. Algae are harvested and beneficial byproducts are retained. Gases, heat and energy produced by energy conversion units are used in units of the system or provided to external sources. Water is cleaned and when separated from the algae and other solids in the algae harvesting unit may be provided to external sources, or may be used in other units of the system. The methods and systems disclosed herein provide for an efficient and substantially complete use of the components of the input biomass.