Problems within agriculture, food, and natural resource (AFNR) systems are increasingly complex, expanding the need for students to develop problem-solving abilities alongside an understanding of their own thinking. In this effort, we explored the problem-solving abilities, metacognition, and systems thinking of current AFNR secondary school students. A descriptive correlational study design was employed. Data were collected via an online, Qualtrics survey. Student responses on the metacognition, systems thinking, and problem-solving ability survey items suggested opportunities for increased focus on these areas throughout their educational experience. In addition, statistically significant relationships between metacognition and systems thinking and systems thinking and problem-solving ability reinforced the importance of these topics within AFNR Education. Recommendations emerging from this work include additional emphasis on metacognition, systems thinking, and problem-solving skills within secondary school AFNR classrooms; utilization of specific strategies to increase systems thinking; operationalizing specific strategies to increase metacognitive knowledge and metacognitive regulation; along with a cross-cutting recommendation for teachers to make their thinking more explicit during instruction to increase metacognition, systems thinking, and problem-solving skills among learners.