We explored the challenges and opportunities in analyzing ancient yeast metagenomes through simulation and comparative genomic techniques. Simulated metagenomes were generated using Gargammel, a tool designed to mimic ancient DNA properties such as fragmentation and damage patterns (notably deamination). Three artificial frequency files were created, each representing different fragment distributions, and combined with varying compositions and damage parameters to simulate realistic ancient beverage-associated microbial communities. The resulting FASTQ reads underwent quality filtering with Fastp, and were subsequently mapped to a concatenated “sensu stricto” reference genome. Further analysis included variant calling, read alignment, and visual inspection using IGV, confirming the integrity and distribution of ancient-like sequencing reads. Nuclear phylogenomic networks were constructed to compare real and in silico datasets, revealing that environmental fungal noise can significantly influence clustering patterns, especially in mitochondrial networks. This observation underscores the complexity of interpreting ancient microbial datasets and highlights the need for careful reference selection. The work emphasizes the importance of simulation in benchmarking genomic pipelines and contributes insight into the evolutionary placement of brewing-related yeasts within ancient fermentation contexts. Future work could refine species composition scripts and extend the approach to polyploid or highly recombinant yeast strains, improving accuracy in ancient metagenomic reconstruction.