Denitrification has a wide range of factors that control its complex regulatory network, one of which is the low concentration of electron donors. In this case the absence of available electrons causes high concentrations of cytotoxic gases (NO and/or N2O) for denitrifying bacteria. The individual adaptive behavior to environmental conditions through different behavior-rules is one of the most powerful aspects of microbial individual-based models. INDISIM-Paracoccus is a model to study P. denitrificans in batch and continuous cultures under both aerobic and anaerobic conditions. The aim of this study was to improve the metabolism sub-model with the introduction of a new individual behavior-rule for this bacterium in order to reduce cytotoxic products with individual mass degradation. A sensitivity analysis for two parameters involved in this behavior-rule, individual cellular maintenance energy and individual mass degradation coefficient, was performed. With this new version of the INDISIM-Paracoccus, implemented in the NetLogo platform, and with a specific combination of the values for these two parameters, the simulation outputs of this computational model, more realistic and mechanistic than other approaches, were in closer agreement with the published experimental data.