The purpose of this paper is to present an observer-based control design with application to continuous bioreactors. For this purpose, phenomenological bioreactor models were represented by identified linear models plus unknown modelling error terms. Therefore, an uncertainty-based observer with a polynomial structure capable of estimating the unknown modelling error of the reactor representation is coupled to a linear input-output controller. The proposed methodology was evaluated in a sulphate reduction bioprocess and an acetone-butanol-ethanol (ABE) fermentation process for butanol (biofuel) production, under continuous regimes. Experimentally validated mathematical models were considered for this purpose. A theoretical framework is presented to demonstrate the corresponding closed-loop stability of the systems, and numerical simulations were carried out to corroborate the satisfactory performance of the proposed methodology.