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11 pages, 7 figures, supplementary materials https://doi.org/10.1016/j.ecolmodel.2021.109731, In a prequel to this paper, we used non-spatial temporal modelling to investigate the impact of non-native ecosystem engineers on a small-scale, intertidal rocky shore in Saldanha Bay, on the west coast of South Africa, where invasive species have changed the physical environment between 1980 and 2015. However, we considered this approach incomplete without the direct inclusion of spatial modelling and zonation. To address this, we compared multiple, layered simulations employing the food-web approach of Ecospace, the spatial-temporal module of Ecopath with Ecosim (EwE). Our simulations included a control; a simulation that restricted drivers to depth and habitat preferences; two simulations to account for structural complexity as a function of the biomass of alien ecosystem engineers – the first indirectly via mediation, and the second via a novel plug-in ‘Ecoengineer’ – and lastly the inclusion of wave action to replicate its effects. Only the simulation that included the Ecoengineer routine matched empirical observations of species diversity indices and the exclusion of the native mussel Choromytilus meridionalis by the arriving alien Mytilus galloprovincialis. Inclusion of mediation did not differ from the model simulation that used only habitat preference and depth to drive the model, and the addition of wave action did not improve model fits. Our results emphasise that when analysing intertidal ecosystems, they should be modelled with an explicit representation of structural habitat complexity over time and space, and we consider that the application of our Ecoengineer plug-in is an effective and novel way of accomplishing this, MC acknowledges partial funding from the European Union's Horizon research program grant agreement No 689518 for the MERCES project, the Institute of Research for Development (IRD, France) and the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019–000928-S) to the Institute of Marine Science (ICM-CSIC)