The impact of inter-group conflict (warfare) on large-scale population declines has long been debated, especially for prehistoric or non-state societies. In this work, we consider that beyond direct battle casualties, which are typically limited, conflicts can also create a “landscape of fear” in which many non-combatants near theaters of conflict abandon their homes and migrate away. This migration has two impacts: It causes population decline in the abandoned regions and increased population density in better protected areas that are targeted by refugees. This higher density, in turn, can place additional stress on local supplies, potentially leading to reduced fertility and increased mortality due to malnutrition and disease. Using both an analytic and agent-based model we investigate the impact of these interactions on population dynamics of small-scale societies. We demonstrate that these indirect effects of conflict are sufficient, even in the absence of combatant casualties, to produce substantial, long-term population boom-and-bust patterns. In particular, our agent-based model is able to account for the large-scale spatial and temporal boom-and-bust patterns observed in radiocarbon data from mid-Holocene Europe. We also demonstrate that greater availability of defensible locations, by acting to protect and maintain the supply of combatants, increases the permanence of the landscape of fear and likelihood of endemic warfare.