The flow of metabolic energy is arguably the most fundamental property governing ecosystem structure. In many microbial communities, particularly those that inhabit environments with little input of exogenous organic matter such as submarine hydrothermal systems and deep subsurface environments, chemolithoautotrophic organisms generate most of the organic matter available to support heterotrophic growth. In these environments, inorganic chemical reactions constitute the main source of energy input to the system, and the conversion of chemical energy to biomass by chemolithoautotrophs exerts a prominent control on the size, composition, and trophic structure of the biological community. A rigorous accounting of energy flow would aid in understanding the potential biological productivity of chemolithoautotrophic communities and help clarify the limits to habitability in geothermal and subsurface environments. In a step towards achieving a more complete accounting of energy flow in such communities, we present here computations to quantify the amount of thermodynamic energy required to synthesize the molecular components of biomass and to compare the relative energy requirements under oxic and anoxic conditions. The results suggest that only about 10% or less of the overall energy consumed during growth by chemolithoautotrophs is transformed directly into biomass. In addition, the results indicate aerobic organisms require approximately 17 kJ (g cells)−1 more energy than anaerobes to synthesize the same biomass. This advantage may help explain why anaerobic organisms appear to yield greater biomass per unit energy input than aerobic organisms in laboratory growth studies, and why anaerobic micro-organisms can exist where the energy yield from catabolism is extremely low.