Cheese rind microbiomes are a validated and stable experimental platform for microbial community research. These communities are relatively simple, reproducible, and easy to grow in the lab. This set of protocols describes how to collect and store cheese rind microbiome samples for isolation of pure cultures, metagenomic sequencing, and other downstream applications. This collection also includes specific protocols for virome extraction and for the isolation of full community and viral-only DNA from cheese samples.