Microbiome studies often overlook eukaryotic species, which have traditionally been targeted using amplicon sequencing of marker genes such as the ITS region. This method has contributed to our understanding of eukaryotic diversity in host-associated and environmental microbiomes. However, it is unable to provide strain-level taxonomic resolution or even differentiate closely related fungal species. Whole metagenome sequencing (WMS) can play a crucial role in differentiating human pathogenic fungi from closely related non-pathogenic species, which is important considering that fungal diseases are responsible for over 1.6 million deaths each year. In our study we used metagenomics to detect human pathogenic fungi (HPF) from compost, a habitat enriched for human pathogens due to its elevated temperature. Our dataset consists of 62 compost samples from public gardens in Berlin and private gardens in Jena. To enable absolute quantification of microbial abundance, we developed and employed a cell-based spike-in composed of one yeast and a gram-negative bacterium. The strains used for the spike-in were selected based on their low abundance and prevalence in European soil samples available in publicly available ITS and 16S datasets. We were able to detect fungi in our metagenomic data and 57% of our samples were positive for Aspergillus fumigatus and 40% were positive for other human pathogenic fungi, including Rhizomucor, Rhizopus, Fusarium, Scedosporium, and Mucor. Our work using shotgun sequencing data will help to better understand the dynamics of HPF in their native habitat. Ongoing work will focus on further characterizing the environmental microbial communities in which these pathogens participate to better understand their ecology and virulence during human infection.