Organic chemistry is very challenging to many students pursuing science careers. Flipping the classroom presents an opportunity to significantly improve student success by increasing active learning, which research shows is highly beneficial to student learning. However, flipping an entire course may seem too daunting or an instructor may simply choose to use this approach selectively. This exploratory, mixed-methods study examines the effectiveness of a partially flipped course in the first semester organic chemistry course. Two sections were taught by the author in Fall 2015: a control section (n = 28 students) using a lecture-based format, and a flipped section (n = 26 students), where 8, 75 min classes (a third of the course) were taught with flipped pedagogy. Significant improvements in test questions on flipped topics were observed, as well as a significant reduction in the course withdrawal rate. While the average overall course grade was similar in the two sections, the flipped section had 25% more A's and B's. Survey and focus group data show that by the end of the semester students in the flipped section felt significantly more confident with the course material than the control section. As measured by student surveys over the course of the semester, students in the flipped section showed a significant change in their preferred type of instruction from lecture to a more collaborative approach, and also showed a significant increase in their comfort level with working in groups and using active learning strategies.