Modern biotechnological laboratories are equipped with advanced parallel mini-bioreactor facilities that can perform sophisticated cultivation strategies (e.g. fed-batch or continuous) and generate significant amounts of measurement data. These systems require not only optimal experimental designs that find the best conditions in very large design spaces, but also algorithms that manage to operate a large number of different cultivations in parallel within a well-defined and tightly constrained operating regime. Existing advanced process control algorithms have to be tailored to tackle the specific issues of such facilities such as: a very complex biological system, constant changes in the metabolic activity and phenotypes, shifts of pH and/or temperature, and metabolic switches, e.g. by product induction, to name a few. In this work we implement a model-predictive control (MPC) approach based framework to demonstrate: 1) the challenges in terms of mathematical model structure, state and parameter estimation, and optimization under highly nonlinear and stiff constraints in biological systems, 2) the adaptations required to enable its application in High Throughput Bioprocess Development (HTBD), and 3) the added value of MPC implementations when operating parallel mini-bioreactors aiming to maximize the biomass concentration while coping with hard constrains on the Dissolved Oxygen Tension profile.Modern biotechnological laboratories are equipped with advanced parallel mini-bioreactor facilities that can perform sophisticated cultivation strategies (e.g. fed-batch or continuous) and generate significant amounts of measurement data. These systems require not only optimal experimental designs that find the best conditions in very large design spaces, but also algorithms that manage to operate a large number of different cultivations in parallel within a well-defined and tightly constrained operating regime. Existing advanced process control algorithms have to be tailored to tackle the specific issues of such facilities such as: a very complex biological system, constant changes in the metabolic activity and phenotypes, shifts of pH and/or temperature, and metabolic switches, e.g., by induction of product formation, to name a few.In this work we implement a model predictive control (MPC) framework to demonstrate: 1) the challenges in terms of mathematical model structure, state and parameter estimation, and optimization under highly nonlinear and stiff dynamics in biological systems, 2) the adaptations required to enable the application of MPC in High Throughput Bioprocess Development (HTBD), and 3) the added value of MPC implementations when operating parallel mini-bioreactors aiming to maximize the biomass concentration while coping with hard constrains on the Dissolved Oxygen Tension profile.