Wildfire affects our planet's biogeochemistry both by burning biomass and by driving changes in ecological communities and landcover. Some plants and ecosystem types are threatened by increasing fire pressure while others respond positively to fire, growing in local and regional abundance when it occurs regularly. However, quantifying total ecosystem response to fire demands consideration of impacts not only on aboveground vegetation, but also on soil microbes like fungi, which influence decomposition and nutrient mineralization. If fire‐resistant soil fungal communities co‐occur with similarly adapted plants, these above‐ and belowground ecosystem components should shift and recover in relative synchrony after burning. If not, fire might decouple ecosystem processes governed by these different communities, affecting total functioning. Here, we use a natural experiment to test whether fire‐dependent ecosystems host unique, fire‐resistant fungal communities. We surveyed burned and unburned areas across two California ecosystem types with differing fire ecologies in the immediate aftermath of a wildfire, finding that the soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. We discovered furthermore that the latter are more strongly altered compositionally by fire than the former, suggesting that differences in fungal community structure support divergent community responses to fire across ecosystems. Our results thus indicate that fire‐dependent ecosystems may host fire‐resistant fungal communities.