Extensive land conversion to agriculture in drylands and associated resource use have wide-ranging impacts on desert ecosystems globally. Incorporating the impacts of human-social aspects is thus imperative in examining ecological interactions. The provision of agricultural inputs in these resource-scarce regions supports invasive and pest species, negatively impacting both agricultural productivity and native desert ecosystems. Understanding the spatial dynamics of invasive and pest species requires analyzing both bottom-up resource availability factors underlying animal distributions and top-down biological controls. Here, we evaluate the social-ecological cascading effects of dryland agriculture on vertebrate pest communities in dryland agricultural communities of Israel. Our study region is characterized by 18 agricultural cooperatives with distinct crop regimes due to contrasting social decision-making and resource allocation schemes (i.e., communal Kibbutzim vs. privatized Moshavim). Crop choices further affect land management (e.g., enclosed vs. open farm systems) and resource intensity. This system is ideal to study trophic mechanisms underlying animal assemblages between agricultural regimes. We examine the role of agricultural land-use practices on pest spatial distributions based on multi-year vertebrate pest observations with agricultural datasets. We use structural equation modelling (SEM) to quantify the relative importance of added agricultural resources underlying bottom-up and top-down trophic processes regulating vertebrate pest assemblages. Results reveal that crop choices determine pest distributions through bottom-up processes directly, while simultaneously driving pest competitive interactions through indirect top-down cascades impacting pest communities. For example, due to the indirect negative effect of wolves on meso-predators (foxes and jackals) mediated by livestock, the total positive effect of livestock on the abundance of meso-predators is reduced. Our study illustrates the social-ecological cascading effects of agricultural regimes on pest community assemblages mediated by contrasting agricultural land-use practices. Considering the expansion of dryland agro-ecological systems globally, understanding the intricate cascading pathways of predator- and prey-pest communities has important implications for agricultural management, biological invasions in drylands and fragile desert environments.