Managed forests represent a major fraction of the global forest area and are known to host impoverished biodiversity compared to natural forests. The effect of forest management has focused mainly on aggregated community metrics such as species richness of single taxa and on simplistic managed vs. unmanaged comparisons. However, the effect of forest management is expected to vary among species and taxa and to be contingent on site-specific conditions. In this study, we focus on fine-scale multi-taxon biodiversity patterns to disentangle the impact of forest management on the forest structure and the abiotic soil conditions of the stands. We base our comparisons on carefully selected pairs of managed and unmanaged stands to minimize regional differences that could confound the effects of management. We found that the total effect of forest management on alpha diversity was positive on plants and rove beetles, neutral on ground beetles and mosses, and negative on crane flies, fungi, and lichens. However, using joint species distribution modeling we show that individual species’ responses to the local underlying soil conditions can be as important as the forest structural changes induced by management, but this varied among the different taxa. Based on these responses we disclose synergies and trade-offs among some of the taxa. Our results indicate that the balance between forest management and abiotic conditions can shape the patterns of forest multi-taxon biodiversity. Considering these conditions can be important in predicting the response of biodiversity to forest management and act as key criteria when prioritizing areas for the conservation of biodiversity.