Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini–Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.