Microbiome composition and function are strongly influenced by its environmental factors, with major shifts driven by intensified anthropogenic pressures over the past centuries. This timeframe extends beyond the scope of traditional experimental and longitudinal studies commonly used to investigate microbiome dynamics. The vast collection of historical samples available in museums and herbaria around the world represent a largely untapped resource for exploring host-microbiome interactions across broader temporal and spatial scales. However, their potential remains underutilized due to incompatibilities with standard analytical pipelines and limited knowledge of optimal classification parameters. While host DNA removal has traditionally considered essential for accurate taxonomic assignment of metagenomic reads, this step is often impractical for many historical samples due to the lack of reference genomes for their host species. Here, we demonstrated that host DNA content does not significantly affect key microbial ecological metrics such as alpha- and beta-diversity. Additionally, metagenomic reads from historical samples are often highly fragmented due to post-mortem degradation. Using k-mer analysis of genomic sequences from hosts and their associated microbiomes, we show that reads as short as 21 bp can still produce reliable results, enabling the recovery of microbial signals that would otherwise be discarded. Overall, this study provides a solid foundation for incorporating natural history collections into host-associated microbiome research, offering valuable insights into the long-term effects of anthropogenic change on microbial communities.