Abstract Background Science in the Learning Gardens (henceforth, SciLG) program was designed to address two well-documented, inter-related educational problems: under-representation in science of students from racial and ethnic minority groups and inadequacies of curriculum and pedagogy to address their cultural and motivational needs. Funded by the National Science Foundation, SciLG is a partnership between Portland Public Schools and Portland State University. The sixth- through eighth-grade SciLG curriculum aligns with Next Generation Science Standards and uses school gardens as the milieu for learning. This provides the context to investigate factors that support success of a diverse student population using the motivational framework of self-determination theory. Results This study reports results from 113 students and three science teachers from two low-income urban middle schools participating in SciLG. Longitudinal data collected in spring of sixth grade in 2015 and fall of seventh grade in 2015 for the same set of students included a measure of students’ overall motivational experiences in the garden (that combined their reports of relatedness, competence, autonomy, and engagement and teacher-reports of re-engagement in garden-based learning activities) to predict four science outcomes: engagement, learning, science grades, and science identity. Findings suggest that garden-based activities show promise for supporting students’ engagement and learning in science classes and in fostering students’ interest in pursuing science long-term. Conclusions As concern for social justice is growing based on the underachievement of students from minority groups, resurgence of the school garden movement over the last several decades provides an opportunity to tip the scales by engaging students in authentic, real-world learning of science and cultivating their interests in science with holistic garden-based learning. This study highlights the role of students’ views of themselves as competent, related, and autonomous in the garden, as well as their engagement and re-engagement in the garden, as potential pathways by which garden-based science activities can shape science motivation, learning, and academic identity in science. Findings also suggest that the motivational model based on self-determination theory can be useful in identifying some of the “active ingredients”—in pedagogy, curriculum, and social relationships—that engage students in these garden-integrated science learning activities.