Most insects harbour endosymbionts that modify their physiology, reproductive mode, and ecology. One fascinating case is in aphids, which host endosymbionts that protect them against attacks from parasitoids. These symbionts are transmitted maternally with high fidelity but can also be transmitted horizontally from infected to uninfected hosts. Since symbionts can confer resistance to their host against parasitoids, levels of symbiont infection should rapidly spread to fixation. This is not the case in most aphid populations that have been studied. Furthermore, the defensive effect of symbionts has been thought to reduce the efficacy of biological control against crop pests, although this has never been properly quantified. We developed a Monte Carlo simulation model to examine changes in levels of endosymbiont infection in an insect population in the presence of parasitoids attacking them over several generations. We also used the model to quantify potential reductions in the efficacy of parasitoids in controlling host populations in biological control. Results suggest that longevity of parasitoids and the spatial aggregation of hosts likely play a major role in the dynamics of symbiont infection. This is the first evidence that these ecological parameters are potentially important for explaining levels of symbiont infection in insect populations.