We took topsoil samples in burned and unburned areas across two California ecosystem types (Sonoma, California, United States) with differing fire ecologies in the immediate aftermath of a damaging wildfire in 2017. From our soil samples, we extracted DNA, amplified and sequenced fungal communities, and also measured chemistry (C%, N% and pH). Soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. The latter are more strongly altered compositionally by fire than the former. This repository contains code to run the analyses we presented in the associated paper (doi: 10.1111/mec.15767), as well as a phyloseq object with the molecular data and a few CSVs with the sample metadata.