Students often struggle to connect concepts with evidence, sometimes because development of research skills has not been emphasized in their science courses. We developed a strategy and protocol to train high school students in research and experimental investigation of questions related to course material on legume biology. The richness of this subject matter allows for adaptations of our framework to address diverse areas of science, including principles in ecology, environmental science, agriculture, microbiology, and evolution. Our framework includes a hands-on classroom inquiry that investigates the symbiotic relationship between nitrogen-fixing rhizobial bacteria and legumes. This student-led, inquiry-based project employs an intellectually demanding, hands-on method of education to build critical research skills using an adaptable model and inexpensive materials. We also report positive student feedback from a post hoc survey to gauge student attitudes toward the activity and the effectiveness of this framework.