A bioprocess operation is commonly determined off-line, in which the measurements contain noise and can affect the controller performance. In this work, a nonlinear controller based on a generalized hyperbolic tangent feedback in the control error was designed, proving reduction of the negative effects caused by noise in the bioreactor measurement output. This was applied to regulate the substrate concentration in a continuous bioreactor for the simultaneous saccharification and fermentation of starch to ethanol. The proposed controller stability was demonstrated by Lyapunov theory. Numerical results showed a good performance by the controller scheme, despite the bounded additive noise in the substrate measurements, and it achieved high ethanol production in comparison with other control laws.