In order to understand some environmental factors that control N2O production by microbes in agricultural soils, a virtual bioreactor for Paracoccus denitrificans was designed using a culture medium containing succinate as a carbon source, ammonium as nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitrogen monoxide and dinitrogen oxide. INDISIM was the core individual-based model for the bacterial behavior and five metabolic pathways were selected and translated into balanced chemical equations using the Thermodynamic Electron Equivalents Model. This thermodynamic approach is the basis of the individual metabolism that this microbe carries out for its cellular maintenance and production of new biomass. The preliminary simulation results achieved with the implementation of this model in NetLogo showed that it is possible to investigate the behavior of this denitrifying bacterium and some of the outputs regarding the temporal evolutions of the diverse substrates are consistent with previous experimental data carried out with it.