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Abstract Despite the central role of saprotrophic fungi in wood decomposition and terrestrial carbon cycling, the diversity and functioning of wood endophytes (i.e. fungi that asymptomatically colonize living plant tissue) on decay remains poorly understood. In a 4‐year field experiment in a boreal forest in the upper midwestern United States, we investigated whether endophytes influenced fungal community structure and subsequent wood decomposition via priority effects. We compared decay of sterilized and non‐sterilized birch ( Betula papyrifera ) logs using both high‐throughput sequencing and wood physiochemical analyses (i.e. density loss, dilute alkali solubility, ratio of lignin loss relative to density loss). Endophyte presence significantly altered initial fungal species composition during the first 2 years and enhanced mass loss over the experiment's duration. Results suggest that following tree death the immediate utilization of organic substrates by wood endophytes significantly alters establishment patterns of later arriving fungal saprotrophs. Independent of endophyte presence, white rot was the wood decay outcome at all sampling times, despite an initial presence of both brown and white rot fungi. Collectively, these findings demonstrate that wood endophytes can affect early community assembly and subsequent decay rates, although environmental filtering leads to consistent selection for fungi with lignin‐targeted decay strategies. A plain language summary is available for this article.