Diverse communities of arthropods and microbes provide humans with essential ecosystem goods and services. Arthropods are the most diverse and abundant macroscopic animals on the planet, and many remain to be discovered. Much less is known about microbial diversity, despite their importance as free-living species and as symbionts. We created “Bugs on Bugs” as an inquiry-based research project in which students investigate both arthropod and microbe diversity by collecting arthropods and culturing their symbionts. “Bugs on Bugs” was developed as a multiple-course project in which students from different disciplines specialize in parts of the project and collaborate in project design and data analysis. We provide instructions for use of “Bugs on Bugs” in active-learning courses, share experiences in which a biodiversity course and a microbiology course completed “Bugs on Bugs” together at our institution, and share suggestions for implementation based on our experiences.