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While increasingly common, school gardens are under-utilized contexts for engaging students in authentic inquiry. Garden ecologies are sufficiently complex, phenomenologically rich and motivated by compelling environmental concerns around sustainable food production. This study reports on findings from a design experiment focused on supporting middle school students as they engaged in scientific inquiry in a school garden in an after-school program. Students developed their own research questions and pursued those questions through empirical investigations. The instructional design supported the transformation of student interests into researchable questions. Analyses characterize the students’ research questions and track the origin and development of students’ research interests. Case study analyses show the varying trajectories of students’ interests and explore the interaction between students’ interests and instruction.