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A key way that STEM (Science, Technology, Engineering and Mathematics) disciplines and agricultural education can be integrated into school-based curriculum and structures, particularly within urban contexts, is via an environmental education (EE) approach. We provide a case example in California of how science and environmental education can be merged in a holistic urban high school program focused on understanding food systems. Specifically, we discuss and apply the concept of environmental action competence (EAC) as a theoretical means of bringing together traditional science education (focused on ecological literacy) with the interdisciplinary and action-oriented focus of environmental education (civics literacy, values awareness and self-efficacy to take action). Using ethnographic methods, we followed 120 students in an urban, comprehensive high school, along with their teachers and community partners during the 2011–2012 and 2012–2013 school years. Interviews with 26 youth and adult participants, were transcribed and coded, then analyzed along with field notes, participant observations, and secondary source data to determine how program elements contributed to the development of students’ EAC. While many students exhibited some of the elements of EAC, only the students who had been in the academy for 3 years were able to base their actions toward the environment in sound ecological reasoning. While program elements supported students’ self-efficacy, students’ ecological understanding was not as well developed. We discuss implications for practitioners, suggesting how EAC can provide a framework to combine the leadership and experiential elements of traditional agricultural and environmental education to support students’ development of STEM competencies.