Abstract Next‐generation sequencing (NGS) has significantly increased knowledge of microbial communities and their distribution. However, it is still not common to apply NGS technology to microbial conservation. We sought to use NGS technologies to evaluate conservation strategies for wood‐inhabiting fungi. Evaluating a deadwood experiment 3 years after it was established, we specifically examined which tree species combinations promoted the highest richness of wood‐inhabiting fungi. Deadwood enrichment was an effective strategy and logs of 6 tree species, either those with the highest wood‐inhabiting fungal α and γ diversity or those with the highest β diversity, maintained >1,000 operational taxonomic units (OTUs) spread over a wide range of taxonomic groups. In comparison, a conservation strategy based only on the results of sporocarp surveys yielded 591 OTUs. This result highlights the need to use NGS approaches to inform microbial conservation strategies. We also determined that 5 tree species with the highest saproxylic beetle γ diversity simultaneously conserved wood‐inhabiting fungi. Apart from deadwood volume, we suggest data on deadwood quality and species also be included as indicators, especially for wood‐inhabiting fungal diversity, and incorporated quickly in forest assessment and monitoring systems in Central Europe.