Changes in preservation conditions act as an important environmental filter driving shifts in microbial communities. However, the precise identities, functional traits, and ecological mechanisms of the dominant agents driving stage-specific deterioration remain insufficiently characterized. This study investigated microbial communities and dominant fungal degraders in waterlogged versus dried bamboo slips using amplicon sequencing, multivariate statistics, and microbial isolation. Results revealed compositionally distinct communities, with dried slips sharing only a small proportion of operational taxonomic units (OTUs) with waterlogged slips, while indicating the persistence of a subset of taxa across preservation states. A key discovery was the dominance of Fonsecaea minima (92% relative abundance) at the water-solid-air interface of partially submerged slips. Scanning electron microscopy (SEM) and pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) indicate that this fungus forms melanin-rich, biofilm-like surface structures, suggesting enhanced surface colonization and stress resistance. In contrast, the fungal community isolated from dried slips was characterized by Apiospora saccharicola associated with detectable xylanase activity. Meanwhile, the xerophilic species Xerogeomyces pulvereus dominated (99% relative abundance) the storage box environment. Together, these results demonstrate that preservation niches select for fungi with distinct functional traits, highlighting the importance of stage-specific preservation strategies that consider functional traits rather than taxonomic identity alone.