This article deals with the design of a fuzzy control strategy for a fluidised bed reactor, which is used for anaerobic wastewater treatment. This strategy is composed of a supervisor system and two PI L/A controllers. In addition, a biomass observer, designed on the basis of the Takagi-Sugeno approach considering a principal component analysis, is used with supervision proposals. The supervisor is also designed following the Takagi-Sugeno methodology; it detects the process state, selects and applies the most adequate control action in order to avoid the washout region. On the other side, two control actions are designed for bicarbonate regulation using the PI/LA technique: adding a base and dilution rate. These control actions, as well as the open loop operation, are selected by the supervisor in order to reject disturbances on the substrate influent allowing at the same time a high methane production. The applicability of the proposed structure in a fluidised bed reactor is illustrated via simulations.