Biotechnology uses enhanced and engineered microorganisms as cell factories to produce high-added values specialty metabolites (e.g. amino acids, vitamins, food additives, biofuels, biofilms, tissues). Biotechnological engineering is of paramount importance for the future of health, chemical, food and other process industries, as well as for the environment. Yet, the current state-of-the-art, characterized by uncertainty and lack of in-depth real-time knowledge about the process state, forces industry to operate their bioprocesses at too conservative, suboptimal and not intensified regimes, so as to avoid undesirable microorganism physiological states. Such practices cause poor efficiency, lack of process stability and increased waste of product and energy. In order to surmount these difficulties, there is a need of identifying desirable metabolic states and of developing bioreactor optimization, monitoring and control methods so as to lead the system to the desired state in the course of a process. The members of our group have been participating in different projects within this line, ranging from biomass growth in fed-batch reactors to lab-scale production of bioplastics, microalgae and tissue.