This study investigated the cognitive effects of the flipped classroom approach in a content-based instructional context by comparing second language learners' discourse in flipped vs. traditional classrooms in terms of (1) participation rate, (2) content of comments, (3) reasoning skills, and (4) interactional patterns. Learners in two intact classes participated and were taught in either a flipped classroom (n = 26) or a traditional classroom (n = 25). In the flipped class, the learners listened to an online lecture before class and participated in a small-group discussion in class. In contrast, the learners in the traditional class listened to a teacher-led lecture in class and then immediately participated in a small-group discussion in class. The learners' discussions were audiorecorded. Quantitative and qualitative analyses indicated no difference in participation rates; however, the students in the flipped classroom produced more cognitive comments involving deeper information processing and higher-order reasoning skills and showed more cohesive interactional patterns than did the students in the traditional classroom. These results indicate that flipped classrooms can effectively promote higher-order thinking processes and in-depth, cohesive discussion in the content-based second language.