The flipped classroom has become a popular pedagogical approach in higher education with its capability to promote students' active engagement in higher-order tasks; nevertheless, studies have shown that the flipped classroom is not always successful. The purpose of this study was to investigate factors including student characteristics as well as learning and teaching factors that influence students' affective and motivational outcomes in flipped classrooms in higher education. A total of 350 university students in 12 different flipped classrooms completed survey instruments at the end of the semester that assessed their experience with flipped classrooms, emotional experiences, and motivation. Results indicated that enjoyment was predicted by the perception of preview materials, teacher facilitation, and participation in learning activities. Boredom was predicted by the perception of preview materials and participation in learning activities. Self-efficacy was significantly explained by both student characteristics and learning and teaching factors. Further discussion and implications are provided.