Herbivores affect vegetation in a variety of ways, involving both trophic and ecosystem engineering interactions, but the study of these different interaction types has rarely been integrated. The aim of this study was to investigate both the trophic and engineering effects of herbivores on plant communities in the Negev desert, Israel, and to promote an integrative approach to the study of herbivore effects in ecosystems. First, we summarise previous studies of the Indian crested porcupine (Hystrix indica), which show that in digging for food, porcupines excavate soil pits, which accumulate resources and seeds resulting in marked changes in plant species richness, density and biomass. By contrast, their trophic effect, via consumption of bulbs, has little impact on populations of perennial plants. Second, we present an empirical study of the trophic and ecosystem engineering effects of harvester ants (Messor spp.). An exclusion experiment, using barriers to restrict ant access, failed to reveal any significant effect of seed collection by harvester ants on plant species incidence (proportional occurrence in samples) or abundance (number of individuals). However, we show that vegetation on nest mounds of M. ebeninus differs in plant density, species richness and biomass from that on undisturbed soil. An analysis of incidence and abundance responses of individual plant species suggests that the observed differences in vegetation resulted from multiple interacting mechanisms. The case studies highlight that many interactions between herbivores and plant communities can occur simultaneously, and that ecosystem engineering and trophic processes can be closely associated, resulting from single actions of herbivores. We propose a conceptual framework that classifies the range of possible trophic and engineering interactions between herbivores and plant communities with respect to the level of association between trophic and engineering effects. The framework is presented as an aid to the design and interpretation of studies of interactions between herbivores and plant communities, and promotes integrative research into the roles of herbivores in ecosystems.