Improving the efficiency of microbial cultivations requires new strategies for process development and optimisation. Conventional approaches, such as “one factor at a time” experimentation, empirical rules for scale-up and process development, and operator-driven process control, are still the standard. While these methods have been proven and found to be effective, they are time- and resource-consuming and lack systemic insight. The utilisation of mathematical models during the process development can reduce process development time and resource consumption. There are several strategies for model-assisted process development and optimisation like model-assisted design of experiments and model-assisted feedback control. Currently, these strategies are mostly used in an academic environment rather than for industrial production. Therefore, a new workflow for the simultaneous process and mathematical model design for microbial cultivations is presented. It includes model-assisted optimisation tools that continuously improve the embedded models during process development. At the same time, these tools help to optimise the process already at the initial stage. Using a new software tool for rapid development of modular mechanistic models, basic model versions are already available at the beginning of bioprocess development. In addition to microbial cultivations, the workflow can also be transferred to enzymatic, biocatalytic processes and cell cultures.