Improvements in technology for the production of microbial biomass from natural gas, which have been gaining importance in recent years, require the development and optimization of energy‐efficient bioreactor designs. The most advanced methods for developing and scaling up industrial biotechnological processes rely on detailed hydrodynamic modeling, in addition to classical approaches, as the main tool for analysis and large‐scale transfer of experimental information. This paper presents the results of a simulation of flows in a bioreactor circuit using the latest mathematical methods and numerical flow analysis tools for two‐phase bubble flows based on experimental data.