This study presents the development and implementation of regulatory control structures in the operation of a Simultaneous Saccharification and Co-Fermentation (SSCF) using Proportional-Integral (PI) controllers. To this end, two different feasible case studies were analyzed: 1) assuming lower cellulose and xylan fractions in the feedstock used to feed the SSCF reactor, and 2) lower efficiency of the microorganism for glucose to ethanol conversion, lower cellulose and xylan fraction content in the feedstock and slightly higher activity of class 1 and 2 enzyme. The implementation of the regulatory control structures showed that it is possible to regulate the process with a simple control system managing those likely uncertainties during the operation of the SSCF unit.