This study demonstrates the need for developing a mathematical model that includes an additional heterotrophic biomass category to describe the biological processes that occur in the presence of a glycerin-based external carbon source (MicroC 2000™). In addition, this study discusses the development of a novel model that describes internalization of glycerin-based MicroC 2000 TM to form glycerol-3-phosphate (G3P) as the internalized component and twostage denitrification by MicroC degraders using G3P. The new mechanistic MicroC model has three new state variables, MicroC degraders (Z MC ), MicroC 2000 TM (S MC ) and internalized component (G3P), 22 rate equations and 8 switching functions. This model was integrated into GPS-X and also merged with the AS/AD model in BioWin® which has 45 state variables, 60 rate equations and 18 switching functions. The model builds on specialist denitrifier concepts, and incorporates the kinetics of glycerin-based chemical oxygen demand (COD) internalization and two-stage denitrification for a specialist population of MicroC degraders (i.e., internalization of MicroC 2000™, nitrate reduction to nitrite and nitrite reduction to nitrogen gas as separate rate equations), as well as aerobic growth and anaerobic decay. The inclusion of aerobic growth and decay of MicroC degraders in the model provides a means to balance the population under non-anoxic conditions, and was validated using lab-scale experimental data. This study also summarizes the validation of the model during high food-to-microorganism (F/M) batch tests as well as during the operation of two parallel nitrate and nitrite fed low F/M sequencing batch reactors (SBRs). Kinetic constants for the model were derived from these batch tests as well as additional SBR and fed batch experiments.