Biofuel cells produce electrical energy from organic materials using electrochemical processes that are catalyzed by biological substances (enzymes or whole microbial cells). In contrast, regular fuel cells use inorganic catalysts (such as platinum) to enhance the electrochemical processes. Most organic substrates (reactants) undergo combustion with the evolution of energy. The biocatalyzed oxidation of organic substrates by oxygen or other oxidizers at two electrode interfaces provides a means for converting chemical energy to electrical energy.

Abundant organic raw materials, such as alcohols, organic acids, or sugars, can be used as substrates for the oxidation process. Molecular oxygen (O₂) or hydrogen peroxide (H₂O₂) can act as the substrate for the reduction process. The organic materials are oxidized at the electrode, called the anode, generating electrons which go through the external electrical circuit to the electrode, called the cathode, where they are accepted by the oxidizer. This process generates the electrical power (voltage and current) released by the biofuel cell. In order to produce continuous electrical power, aqueous solutions containing the organic fuel and the oxidizer are pumped to the respective electrodes in the biofuel cell, where these electrochemical processes take place.