The flipped classroom approach has increasingly been implemented in higher education and has shown promise for enhancing learning processes across many domains. In this instructional method, learners use certain learning materials to prepare for in-class lessons focusing on a deeper understanding and application of knowledge. Feedback and peer interaction are known to be able to facilitate such higher-order processing. However, questions remain about the extent to which they can enhance the effectiveness of flipped classrooms in higher education. To examine these questions, we employed a 2 × 2 quasi-experimental design in a flipped classroom course on empirical research methods in the social sciences (N = 105). We investigated the effects of the type of feedback (knowledge of correct response vs. elaborated) during a quiz on declarative knowledge, and peer interaction during an application-oriented exercise (individual learning vs. cooperative learning). Elaborated feedback exerted a significant, medium-sized effect on declarative and application-oriented knowledge. A mediation analysis showed that about half of the effects of the type of feedback on application-oriented knowledge were mediated by declarative knowledge. The results implicate elaborated feedback as an effective tool for fostering declarative knowledge acquisition in flipped classrooms. Subsequently, this process also positively influences the formation of application-oriented knowledge during the in-class learning phases.