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Summary Priority effects among wood decomposers have been demonstrated by manipulating fungal assembly history via inoculations in dead wood and then tracking community development using DNA sequencing. Individual wood‐degrading fungi have been shown, however, to initiate decay after having colonized living trees as endophytes. To track these ‘upstream’ colonizers across the endophyte–saprophyte transition, we coupled high‐throughput sequencing with wood physiochemical analyses in stem sections extracted from healthy birch trees ( Betula papyrifera ; 4–7 cm dia.). We incubated wood in microcosms, limiting communities as endophytes−only or challenging endophytes with Fomes fomentarius or Piptoporus betulinus at high exogenous inoculum potential. Initial fungal richness in birch stems averaged 143 OTU s and decreased nearly threefold after five months of decomposition. Although F. fomentarius successfully colonized some stem sections incubated at 25 °C, decayed wood was generally dominated by saprophytic fungi that were present originally in lower abundances as endophytes. Among saprophytes, fungi in the brown rot functional guild consistently dominated, matching wood residues bearing the chemical hallmarks of brown rot. Despite this functionally redundant outcome, the taxa that rose to dominate in individual sections varied. Surprisingly, the brown rot taxa dominating wood decomposition were better known for lumber degradation rather than log decay in ground contact. Given the isolation from colonizers in our design, this redundancy of brown rot as the outcome suggests that these taxa and more generally brown rot fungi could have adapted to decompose wood where there is lower competitive pressure. Competitive avoidance would complement the diffuse depolymerization mechanisms of brown rot fungi, which are likely more prone to sugar pilfering by other organisms than the processive depolymerization mechanisms of white rot fungi. Overall, this guild‐level predictability of fungal endophyte development and consequence is encouraging given the challenges of predicting wood decomposition, and it provides a base for testing these dynamics under increasing natural complexity.