This release archives the R scripts used for the microbiome analysis of Euperipatoides rowelli gut samples across deadwood microhabitats in the Tallaganda forest. Contents R scripts for: Alpha diversity Beta diversity and ordinations DESeq2 differential abundance Core microbiome and prevalence Relative abundance summaries (Phylum–Genus) UpSet and other compositional plots Master script to generate publication-ready figures. Example input files (metadata, OTU/ASV table, taxonomy, tree) matching the manuscript. Intended use These scripts are provided to support transparency and reproducibility of the associated velvet worm gut microbiome study. Users can adapt the workflow to related host–microbiome datasets with similar structure. A Zenodo DOI will be associated with this release for long-term archiving and citation.