This dataset includes the diversity of soil prokaryotes, fungi and micro-eukaryotes in unmanaged forest reserves with managed forests across nine locations within Switzerland. Forests have been exploited for resources for centuries, which has caused disturbances, altered community structure, and reduced diversity at different scales. Strict forest reserves, where no forest management is practiced, have been implemented to promote biodiversity, by allowing old trees with microhabitats and high deadwood amounts. However, the effectiveness of forest reserves on soil microbial diversity and functional traits are little known at a national scale in Swiss forests. The associated metadata includes local environmental conditions, such as soil pH, organic C, N, deadwood volume, MAT and MAP, and forest type (coniferous vs deciduous).