Oral biofilms are now appreciated as crucial components of homeostatic states characterizing oral health and dysbiotic shifts underlying oral diseases. In fact, the two most common chronic oral diseases, dental caries and periodontal diseases, are best understood as microbiome imbalances in supragingival and subgingival niches, respectively. Despite notable scientific advances in the last decade, a comprehensive understanding of compositional and functional aspects of oral biofilm microbiomes remains elusive. The advent of culture-independent, high-throughput sequencing methods has transformed our ability to measure previously unknown aspects of oral microbiomes—metagenomics, metatranscriptomics, metaproteomics, and metabolomics, collectively referred to as “omics” have the potential to provide unprecedented insights in biofilm biology and its interface with the human host and its environment. This chapter introduces fundamental concepts of omics applications in the study of oral disease-associated biofilms and presents 10 important considerations regarding associated clinical phenotypes, sample collection and processing, bioinformatics pipelines, overall study design, and inference. Additionally, we present the outline of a comprehensive multi-omics discovery pipeline that has been recently employed for the study of pediatric oral health and emphasize that attention to rigor and reproducibility is key for maximizing biological insights from such omics applications.