The estimation of biomethane or biohydrogen yield is used to evaluate energy recovery during the process of the anaerobic treatment of waste and wastewater. Mathematically calculated theoretical values can also be used in biomethane or biohydrogen potential tests as reference points to calculate which fraction of substrate is decomposed, when the substrate degradation stopped and when the sample’s self-digestion begins. This study suggests expanded forms of equations for anaerobic processes leading to either biomethane or biohydrogen. The traditional equations describing the conversion of a substrate with known carbon, hydrogen, oxygen and nitrogen composition were expanded to account for the composition of sulfur (for biohydrogen yields) and phosphorus (both biohydrogen and biomethane yields). As an optional part, one metal cation was also incorporated into the chemical formula of the evaluated wastewater composition in case the compound of biodegradable interest exists as a salt. The equations derived here can be useful for researchers estimating energy recovery based on the elemental analysis of samples, such as algal biomass harvested during harmful algal blooms (HABs). Examples of biomethane and biohydrogen yield estimations from sulfur- and phosphorus-containing compounds are also provided.