Background: The decomposition of organic matter is among the most important ecosystem processes in forest ecosystems, regulating the carbon and nutrient cycle. However, our understanding about how direct (environment and decomposer diversity) and indirect effects (environment via decomposer diversity) contribute to deadwood decomposition is limited. We set up a large real-world deadwood experiment in a mixed mountain forest in southeastern Germany considering beech (Fagus sylvatica) and fir (Abies alba) as substrates. We simultaneously tested effects of canopy cover, amount and heterogeneity of surrounding deadwood and a broad set of fungal diversity measures mediated by environment on deadwood density loss after 10 years. Results: Deadwood density loss was mainly explained by tree species and canopy cover. Beech showed higher density loss than fir and density loss was larger in open compared to closed canopies. Even though fungal diversity is mediated by environment, the direct effects on density loss were weak and inconsistent across tree species and fungal diversity measures. Conclusions: We found weak support for the fungal diversity–ecosystem process relationship for deadwood decomposition. We suggest that deadwood decomposition and the resulting carbon and nutrient cycles in forest ecosystems are primarily regulated by the tree species selected through forest management and canopy disturbances, particularly in the context of climate change.