Critical thinking (CT) underpins the analytical and systems-thinking capacities needed for effective conservation in the 21st century but is seldom adequately fostered in most postsecondary courses and programs. Many instructors fear that devoting time to process skills will detract from content gains and struggle to define CT skills in ways relevant for classroom practice. We tested an approach to develop and assess CT in undergraduate conservation biology courses using case studies to address both challenges. We developed case studies with exercises to support content learning goals and assessment rubrics to evaluate student learning of both content and CT skills. We also developed a midterm intervention to enhance student metacognitive abilities at a light and intensive level and asked whether the level of the intervention impacted student learning. Data from over 200 students from five institutions showed an increase in students’ CT performance over a single term, under both light and intensive interventions, as well as variation depending on the students’ initial performance and on rubric dimension. Our results demonstrate adaptable and scalable means for instructors to improve CT process skills among undergraduate students through the use of case studies and associated exercises, aligned rubrics, and supported reflection on their CT performance.