Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8-week metagenomics laboratory course has the objective of introducing upper-level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high-throughput sequencing before transitioning to computer-based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre- and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting-edge field of metagenomics.