Herein, we describe the results of a Flipped Classroom (FC) teaching approach implemented at a university to enhance the student learning of stereochemistry concepts across various academic programs. The academic activity research comprised three stages: design, implementation, and evaluation. During the first phase, we designed educational tools with Genially for preclass activities and Nearpod for in-class sessions, both as free access platforms. Subsequently, we engaged 106 students in the FC method for learning stereochemistry, conducting preclass and face-to-face activities. The impact of this approach was determined on both the operational and academic aspects. The operational assessment indicated a high level of acceptance with positive feedback on the interactive platform's interface (72–95%), content relevance (41–90%), and student perception (44–91%). Through several activities, we evaluated students' grasp of academic content and professional skills. Comparing the performance of the experimental and control groups, it was evident that students in the FC group achieved better results. The overall grades revealed that 100% of the experimental group passed the workshops, 87% passed the interactive activities, and 94% passed the knowledge test. In contrast, in the control group, only 72% passed the final evaluation test. Overall, the performance of the control group was consistently lower compared with the experimental group across all activities.