Human activities have led to massive influxes of pollutants, degrading the habitat of species and simplifying their biodiversity. However, the interaction between food web complexity, pollution and stability is still poorly understood. In this study we evaluate the effect exerted by accumulable pollutants on the relationship between complexity and stability of food webs. We built model food webs with different levels of richness and connectance, and used a bioenergetic model to project the dynamics of species biomasses. Further, we developed appropriate expressions for the dynamics of bioaccumulated and environmental pollutants. We additionally analyzed attributes of organisms’ and communities as determinants of species persistence (stability). We found that the positive effect of complexity on stability was enhanced as pollutant stress increased. Additionally we showed that the number of basal species and the maximum trophic level shape the complexity–stability relationship in polluted systems, and that in-degree of consumers determines species extinction in polluted environments. Our study indicates that the form of biodiversity and the complexity of interaction networks are essential to understand and project the effects of pollution and other ecosystem threats.