A mathematical model, named A3DX, based on ASM3(A3) for C and N removal, on the bio-P metabolic model of the Technological University of Delft (D), and on extra processes (X) for chemical and biological phosphorus removal, was developed and used to simulate the treatment of a fermented cheese factory effluent by a sequencing batch reactor (SBR). Experimental data obtained from a pilot-scale SBR were used to calibrate the model. The model calibration was performed by changing a minimal number (four) of default values for parameters, and by introducing a Monod function to account for magnesium limitation. This study suggests that the value of stoichiometric and kinetic model parameters determined with municipal effluents or enriched bio-P cultures can be reasonably used with some agro-industrial effluents with minimal parameter adjustment for calibration.