An integrated system produces ethanol and biogas from raw plant materials. The system includes a pretreatment apparatus for converting raw plant materials into sugars and a fermenter for fermenting the sugars to produce a beer including ethanol. A distillation apparatus separates the beer into the ethanol and a whole stillage, and a separator then separates the whole stillage into a thin stillage and wet distillers grains. A biogas apparatus processes a first portion of the thin stillage to produce biogas and a biogas effluent, and converts a percentage of the non-fermentable solids and organic acids in the thin stillage into biogas. The pretreatment apparatus is supplied with an amount of fresh water and an amount of backset, the backset including the biogas effluent recycled from the biogas apparatus to the pretreatment apparatus.