The laboratory and computational tools available to microbiome researchers have greatly improved in recent years, especially in assembling genomes from complex communities. Most of the research to date has focused on macrodiversity, which is classical ecology metrics like population abundance, α-diversity, and β-diversity. But microdiversity — population genetics metrics like single nucleotide polymorphisms (SNPs) and selective pressures — is important to consider. There are several technical and accessibility issues that hinder widespread analysis of microdiversity in metagenomic datasets, but the recently developed open-access software tool MetaPop is designed to close this gap. MetaPop provides a user-friendly interface to analyze both the macro- and microdiversity of microbial and viral community metagenomes. For small datasets, MetaPop can be run on a laptop, making it a practical choice for non-bioinformaticians or labs without access to high-powered computing. Researchers demonstrated MetaPop's utility by analyzing the viromes of autistic children who underwent fecal microbiota transplants. The only significant differences found were microdiversity metrics, not macrodiversity, which highlights how standardized microdiversity analyses may be invaluable for maximizing biological inferences in metagenomics research. Overall, MetaPop represents a useful workflow that combines classical community ecology and population genetics tools in a single integrated pipeline.