The start-up phase of a membrane bioreactor (MBR) for municipal wastewater treatment was studied to determine the effect of temperature on the organic matter removal and heterotrophic kinetics. The MBR system was analyzed during four start-up phases with values of hydraulic retention time (HRT) of 6 h and 10 h, mixed liquor suspended solids (MLSS) concentrations of 4,000 mg L−1 and 7,000 mg L−1 in the steady state, and temperature values of 11.5, 14.2, 22.9 and 30.1 °C. The influence of temperature on the biological process of organic matter removal was determined through the Arrhenius equation and Monod model. At the most favorable operation conditions of HRT (10 h) and MLSS (7,000 mg L−1) corresponding to phase 4, the effect of these variables dominated over the temperature. Heterotrophic biomass from phase 2 (HRT = 10 h, MLSS = 4,000 mg L−1 and T = 30.1 °C) had the highest values of chemical oxygen demand (COD) degradation rate (rsu,H), implying less time to remove organic matter and shorter duration of the start-up phase.