Academic misconduct is a serious issue among college students, and integrating academic ethics into major courses is expected to help prevent, dissuade, and respond to this issue. With the widespread adoption of flipped classrooms in higher education, it is necessary to explore effective ways to integrate academic ethics into flipped major courses. This study applied an innovative approach to integrate academic ethics into a flipped chromatographic analysis course and investigated the instructional effectiveness of this approach based on students' ethical awareness and ability and course satisfaction. A quasi-experimental study with a nonequivalent pre/post-test control group design was conducted on a sample of 203 students (102 in the experimental group and 101 in the control group). Data were collected by means of online questionnaires and analyzed with descriptive and inferential statistics. Five topics in academic ethics were integrated into the teaching of the experimental group. The results showed that the experimental and control groups were homogeneous before the intervention. At the end of the course teaching, students in the experimental group were found to have stronger awareness and ability for academic integrity, but their course satisfaction did not differ from that of the control group. These findings suggest that academic ethics can be integrated into a flipped major course to effectively improve students' awareness and ability of academic integrity without compromising students' overall satisfaction with the course. Improving students' satisfaction with a flipped course requires considering both course and student characteristics as the latter may have a greater impact than the former.