Forests store carbon in downed logs, whose decomposition is driven by bacterial and fungal communities. Yet most studies treat individual logs as homogeneous units, obscuring internal–external gradients in wood chemistry as fine-scale habitat filters. To address this gap, we combined ALDEx2, SpiecEasi networks, Mantel tests and PLS-SEM on 24 samples from Larix principis-rupprechtii logs spanning three decay stages (I, III, and V) and two radial positions. Chemical heterogeneity between positions peaked at Stage III (5.9-fold difference in total nitrogen), with severe internal nitrogen and phosphorus depletion. Bacterial alpha diversity converged between positions by Stage V, whereas fungal communities maintained persistent divergence, and differentially abundant taxa showed stage- and position-associated enrichment patterns. Network topology did not differ detectably between internal and external wood. Path modelling showed contrasting associations: fungal composition tracked primarily the decay-stage axis, whereas bacterial composition was associated more weakly and mainly through an indirect nutrient channel. These results provide a fine-scale, descriptive account of divergent bacterial and fungal responses to within-log heterogeneity during downed-log decomposition in a temperate coniferous forest.