It is well-known that secondary metabolite production is repressed by excess nitrogen substrate available in the fermentation media. Although the nitrogen catabolite repression has been known, quantitative process models have not been reported to represent this phenomenon in complex medium. In this paper, we present a cybernetic model for rifamycin B production via Amycolatopsis mediterranei S699 in complex medium, which is typically used in industry. Nitrogen substrate is assumed to be present in two forms in the medium; available nitrogen (S(ANS)) such as free amino acids and unavailable nitrogen (S(UNS)) such as peptides and proteins. The model assumes that an inducible enzyme catalyzes the conversion of S(UNS) to S(ANS). Although S(ANS) is required for growth and product formation, high concentrations were found to inhibit rifamycin production. To experimentally validate the model, five different organic nitrogen sources were used that differ in the ratio of S(ANS)/S (UNS). The model successfully predicts higher rifamycin B productivity for nitrogen sources that contain lower initial S(ANS). The higher productivity is attributed to the sustained availability of S(ANS) at low concentration via conversion of S(UNS) to S(ANS), thereby minimizing the effects of nitrogen catabolite repression on rifamycin production. The model can have applications in model-based optimization of substrate feeding recipe and in monitoring and control of fed batch processes.