This paper examines the importance of influent fractionation, kinetic, stoichiometric and mass transfer parameter uncertainties when modeling biogas production in wastewater treatment plants. The anaerobic digestion model no. 1 implemented in the plant-wide context provided by the benchmark simulation model no. 2 is used to quantify the generation of CH<sub>4</sub>, H<sub>2</sub> and CO<sub>2</sub>. A comprehensive global sensitivity analysis based on (i) standardized regression coefficients (SRC) and (ii) Morris' screening's (MS's) elementary effects reveals the set of parameters that influence the biogas production uncertainty the most. This analysis is repeated for (i) different temperature regimes and (ii) different solids retention times (SRTs) in the anaerobic digester. Results show that both SRC and MS are good measures of sensitivity unless the anaerobic digester is operating at low SRT and mesophilic conditions. In the latter situation, and due to the intrinsic nonlinearities of the system, SRC fails in decomposing the variance of the model predictions (R<sup>2</sup> <0.7) making MS a more reliable method. At high SRT, influent fractionations are the most influential parameters for predictions of CH<sub>4</sub> and CO<sub>2</sub> emissions. Nevertheless, when the anaerobic digester volume is decreased (for the same load), the role of acetate degraders gains more importance under mesophilic conditions, while lipids and fatty acid metabolism is more influential under thermophilic conditions. The paper ends with a critical discussion of the results and their implications during model calibration and validation exercises.