This study adopts a qualitative method in comparing EFL students' development of metacognitive knowledge and metacognitive strategy use in a university flipped classroom, as opposed to a regular classroom context. A total of 8 students (4 from each class) were each interviewed twice, once at the beginning and again at the end of the semester, in semi-structured interviews. Findings show that, in the context of a flipped classroom, learners' metacognitive knowledge had undergone qualitative changes over the course of a semester. Similarly, the flipped classroom design had led to a more active, deeper use of metacognitive strategies. Finally, implications for teaching and further research are discussed.