Single-cell genomics is a powerful tool for recovering the genome sequences of the uncultivated species comprising complex microbial communities. The laboratory procedure typically involves sorting individual microbial cells into reaction wells before performing whole-genome amplification. Here, we provide an overview of laboratory steps such as sample preservation, single-cell sorting, and performing whole-genome amplification reactions. We also discuss common challenges and provide suggestions for dealing with problems such as DNA contamination that can derail single-cell genomics studies.