Agricultural farming is a major consumer of global arable lands and has a direct effect on species decline through habitat destruction. However, agricultural endeavours can also evoke indirect threats that will result in behavioural modifications of indigenous species. In a desert ecosystem, where a political border led to a farming dichotomy between intensive cultivates in Israel and intact lands in Jordan, we compared the foraging behaviours and abundances of the red fox and two species of gerbils, close to and distant from farms, and during two moon phases. We estimated fox and gerbil foraging levels by track counts, and measured gerbil time allocation, vigilance and apprehension by the giving-up density method. While foxes were significantly more abundant and active at locations close to farms, gerbils were significantly more abundant and active at locations distant from farms. Moreover, the typical reduction in food consumption during full-moon nights was exhibited only at locations close to farms. These results could suggest that indicators of predation risk, such as illumination intensity or distance to cover, are not universal, and their effectiveness may depend indirectly on anthropogenic activities, such as agricultural farming. The results could also suggest that although intensive agricultural endeavours benefit foxes, they might increase the predatory pressure on gerbils in addition to the already known effects of habitat loss. Therefore, agriculture acts as a double-edged sword by reducing natural habitats, while at the same time changing the predator–prey natural balance.