A model for the biodegradation of non-ionic surfactants in an activated sludge system during acclimatisation was developed, based on respirometric and titrimetric experimental data. The data were obtained in a sequencing batch reactor (SBR) using a non-ionic surfactant as sole carbon source and sludge previously acclimatised to a different surfactant. The model was successfully applied to successive SBR-cycles of sludge acclimatisation processes subjected to two ethoxylated surfactants. The model was validated using the corresponding total organic carbon data. The evolution of the model parameters along the acclimatisation process was examined. An acclimatisation model was developed using the evolution of two of these parameters (affinity constant and inhibition constant), supported by two independently calculated acclimatisation indicators. This acclimatisation model was then applied to determine an optimal surfactant concentration sequence to feed non-acclimatised sludge during a period of 41 days, in order to induce pre-acclimatisation to this surfactant before it replaces another one in the wastewater. The model was also useful in the economical assessment of this and alternative procedures to cope with frequent changes in activated sludge feed composition.