The most important initial issue when considering the application of anaerobic digestion systems is the feedstock to the process. Digesters typically can accept any biodegradable material; however, if biogas production is the aim, the level of putrescibility is the key factor in its successful application. The more putrescible the material the higher the gas yields possible from the system. Substrate com­position is a major factor in determining the methane yield and methane pro­duction rates from the digestion of biomass. Techniques are available to determine the compositional characteristics of the feedstock, while parameters such as solids, elemental and organic analyses are important for digester design and operation.

Anaerobes can break down material to varying degrees of success from readily in the case of short chain hydrocarbons such as sugars, to over longer periods of time in the case of cellulose and hemicellulose. Anaerobic microorganisms are unable to break down long chain woody molecules such as lignin. Anaerobic digesters were originally designed for operation using sewage sludge and manures. Sewage and manure are not, however, the material with the most potential for anaerobic digestion as the biodegradable material has already had much of the energy content taken out by the animal that produced it. Therefore, many digesters operate with co-digestion of two or more types of feedstock. For example, in a farm-based digester that uses dairy manure as the primary feedstock the gas production may be significantly increased by adding a second feedstock; e. g. grass and corn (typical on-site feedstock), or various organic by-products, such as slaughterhouse waste, fats oils and grease from restaurants, organic household waste, etc. (typical off-site feedstock).

A second consideration related to the feedstock is moisture content. Dryer, stackable substrates, such as food and yard wastes, are suitable for digestion in tunnel-like chambers. Tunnel style systems typically have near-zero wastewater discharge as well so this style system has advantages where the discharge of digester liquids are a liability. The wetter the material the more suitable it will be for handling with standard pumps instead of energy intensive concrete pumps and physical means of movement. Also the wetter the material, the more volume and area it takes up relative to the levels of gas that are produced. The moisture content of the target feedstock will also affect what type of system is applied to its treatment. In order to use a high solids anaerobic digester for dilute feedstocks, bulking agents such as compost should be applied to increase the solid content of the input material. Another key consideration is the carbon:nitrogen ratio of the input material. This ratio is the balance of food a microbe requires in order to grow. The optimal C:N ratio for the ‘food’ of a microbe is 20-30:1. Excess N can lead to ammonia inhibition of digestion.

The level of contamination of the feedstock material is a key consideration. If the feedstock to the digesters has significant levels of physical contaminants such as plastic, glass or metals, then pre-processing will be required in order for the material to be used. If it is not removed then the digesters can be blocked and will not function efficiently. It is with this that mechanical biological treatment plants are designed. The higher the level of pre-treatment a feedstock requires, the more processing machinery will be required and hence the project will have higher capital costs.