This study examines EFL students' metacognitive strategy use in a university flipped classroom and the underlying factors of metacognitive strategy use. The participants in our study were students enrolled in an elective English course at a university in Taiwan, where they had to watch online course videos outside of class and participate in activities that required knowledge application. Students' metacognitive strategy use and factors affecting their use were elicited through written accounts, class observations, and semi-structured interviews. Findings show that factors affecting their metacognitive strategy use include students' expected learning outcome and peer learning. Students' greater control over learning in a flipped classroom context further facilitates their metacognitive strategies. Finally, possible directions for metacognitive instruction are discussed.