At the present, many researches work in the application of different control techniques in complex systems as the biotechnological processes, included intelligent control techniques. In this work, it is approached the modeling and control of bio-reactors (complex, no linear and variants-with-time systems), where the fermentation process of Pichia pastoris occurs as part of vaccines production in “Centro de Ingeniería Genética y Biotecnología” (CIGB). Specifically, we work with antihepatitis-B vaccine production (CIGB-Havana) and bovine vaccine production (CIGB-Camagüey) processes. To carry out the work, models are used to estimate methanol concentration and cellular growth respectively and models of control loop elements are determined. For each operation point that the technologists wanted to control, PID regulators were designed and several strategies are applied for processes control, among those gain schedule based on fuzzy logic that commutes the controllers among the operation points is stand out. In the results, improvements are appreciated in temporary response of controlled system and it is possible to maintain the controlled variables inside established values.