Phylogenomics is the inference of phylogenies using genome-scale data. In a broader sense, it is also the mapping of genomic patterns onto phylogenies. This process is inherently complex, requiring the concurrent use of genomic, bioinformatics, phylogenetics, and comparative methods expertise. Here, we provide an overview of how to plan and conduct a typical phylogenomic study of insects aimed at both producing a genome-scale phylogenetic tree and studying various genomic traits on that phylogeny. Drawing from our experience in insect phylogenomics, we offer practical recommendations to guide researchers through this effort.