Although fire is an annual occurrence in savanna systems and is widely used as a tool in conservation management, the effects of fire on biodiversity remain poorly understood. This study investigated the response of ant assemblages, a key component of invertebrate diversity, to burning in two dominant savanna ecosystems (spinifex uplands and sandplain) in the Australian semi-arid tropics. A total of 180 pitfall traps were established in each habitat and each sampling period (wet and dry season). We collected a total of 89 046 ants from 18 genera, representing 126 species. The response of ant assemblages to fire varied with habitat type. We relate this response to habitat-specific fire induced differences in microhabitat structure and the vertical distribution of biomass. There were large differences in assemblage composition in the spinifex habitat, where vegetation composition and structure varied considerably between burnt and unburnt sites. In contrast, assemblages were largely resilient to single fire events in the sandplain, where vegetation change following fire was less pronounced. This study highlights the need for conservation managers to be aware of how different habitats respond to fire and what the consequences of different management actions might be.