In the natural world, faces are not isolated objects but are rather encountered in the context of the whole body. Previous work has studied the perception of combined faces and bodies using behavioural and electrophysiological measurements, but the neural correlates of emotional face–body perception still remain unexplored. Here, we combined happy and fearful faces and bodies to investigate the influence of body expressions on the neural processing of the face, the effect of emotional ambiguity between the two and the role of the amygdala in this process. Our functional magnetic resonance imaging analyses showed that the activity in motor, prefrontal and visual areas increases when facial expressions are presented together with bodies rather than in isolation, consistent with the notion that seeing body expressions triggers both emotional and action-related processes. In contrast, psychophysiological interaction analyses revealed that amygdala modulatory activity increases after the presentation of isolated faces when compared to combined faces and bodies. Furthermore, a facial expression combined with a congruent body enhanced both cortical activity and amygdala functional connectivity when compared to an incongruent face–body compound. Finally, the results showed that emotional body postures influence the processing of facial expressions, especially when the emotion conveyed by the body implies danger.