In this article, bench-scale heat flux calorimetry is applied to monitor complex microbial systems producing secondary metabolites and having a theologically complex behavior. With such systems, biological metabolic activity can only be measured accurately if calorimetry is improved by on-line correction for stirring power variations using torque measurement.First, a successful application to the production of the antibiotic erythromycin by Saccharopolyspora erythraea is presented. During a batch-culture study, it was shown that heat-flux calorimetry can indicate the two main phases of the process, the exact moment of any substrate depletion, and the nature of the depleted substrate. A fed-batch strategy was set up to optimize erythromycin production. Cultures controlled by calorimetry with pulsed addition of the N-source during the trophophase and of the C-source during the idiophase allowed a higher productivity to be reached.Second, an application of heat-flux calorimetry to the production of a bioinsecticide by the sporulating bacterium Bacillus sphaericus is presented. This project aims to understand, model and control the factors that effect growth, sporulation and insecticide production in a chemically defined medium. A batch-culture study has shown that calorimetry can be used to monitor the different phases of the process (growth, sporulation) and the different substrate depletions. The use of a control strategy to optimize production of the insecticidal protein is now under investigation.