Forest ecosystems face increasing pressure from the growing demand for wood and global change, yet the ecological consequences of management decisions remain incompletely understood. Deadwood is a key component in forest ecosystems, supporting biodiversity and biogeochemical cycles. However, the role of deadwood characteristics, the abiotic environment, and its interactions for fungal and bacterial diversity is not fully understood. We experimentally assessed how different combinations of key deadwood characteristics influence microbial diversity and community assembly, using both molecular (within wood) and fruit body sampling. Four types of logs (soil-contacting, non-soil-contacting, debarked, and bark-intact) were placed under open and closed canopies to manipulate strong contrasts in microclimatic conditions. We found that bark retention had a stronger effect on microbial alpha and beta diversity than soil contact or canopy cover. Debarking increased fungal and bacterial molecular diversity (e.g., fungal richness increased by ∼20 OTUs per log on average) while decreasing phylogenetic diversity more than expected, indicating abiotic selection of narrower but species-rich lineages. Fungal fruit body diversity showed a contrasting pattern with an increased diversity under open canopies, barked trees, and soil contact, suggesting a combination of enhanced fruiting cues and benign growing conditions. Observed patterns were largely explained by differences in deadwood moisture conditions. To maintain microbial diversity across multiple facets, it is crucial to vary both soil contact and bark retention when enriching deadwood. Management approaches that prioritize characteristics enhancing only alpha diversity may inadvertently reduce phylogenetic diversity and, consequently, functional potential.