Biochar and manure can be used for sustainable land management. However, little is known about how soil amendments might affect surface- and below-ground microbial processes and subsequent wood decomposition. In a split-split-split plot design, we amended soil with two rates of manure (whole plot; 0 and 9 Mg ha^-1) and biochar (split-plot; 0 and 10 Mg ha^-1). Wood stakes of three species (hybrid poplar, triploid Populus tomentosa Carr.; aspen, Populus tremuloides Michx.; and pine, Pinus taeda L.) were placed in two positions (horizontally on the soil surface, and inserted vertically in the mineral soil), which served as a substrate for fungal growth. In 3 years, the decomposition rate (mass loss), moisture content, and fungal community (via high-throughput sequencing methods) of stakes were evaluated. Results indicated that biochar and/or manure increased the wood stake decomposition rates, moisture content, and operational taxonomic unit (OTU) abundance. However, the richness and diversity of fungi were dependent on wood stake position (surface > mineral), species (pine > the two Populus), and sample dates. This study highlights that soil amendment with biochar and/or manure can alter the fungal community, which in turn can enhance an important soil process (i.e., decomposition).