Common digester misconceptions include that anaerobic digestion and the resulting biogas production will reduce the quantity of manure and the amount of nutrients that remain for utilization or disposal - an anaerobic digester DOES NOT MAKE MANURE DISAPPEAR! Often the volume of material handled from a digester increases because of required dilution water for satisfactory pumping or digester operation. On an average, only 4% of the influent (volatile solids) is converted to biogas. The remaining 96% leaves the digester as a stable nutrient rich, weed seed free, reduced or pathogen free and nearly odorless effluent. This means that a farm loading 1000 gallons per day into a digester can expect to have 960 gallons of material to store and ultimately utilize. Depending on digester design and operation, solids can also settle out in the bottom of the digester and/or form a floating scum mat. Both the scum mat and the solids will eventually need to be mechanically removed from the digester to assure desired performance. When evaluating the actual performance and operation of a digester it is important to determine and account for the amount and type of material retained in the digester and the cost of lost digester volume and ultimate cleaning.

Manure and other decomposing organic matter can produce hydrogen sulfide, a deadly gas that settles to the bottom of pits, sumps and tanks.