An inquiry-based laboratory learning unit was designed to enhance high school students' understanding of the application of lipase as a catalyst to synthesize isoamyl and geranyl ester derivatives as well as to promote their understanding and positive perceptions of green chemistry. The learning unit consisted of three laboratories and a final presentation. The first laboratory activity allowed students to learn how to adjust macroscale titration techniques to microscale titration techniques so that the method could be used for quantitative determination of ester products in the next two laboratory activities. The second laboratory activity introduced students to a greener way to synthesize ester compounds by replacing a harmful strong acid catalyst with a more environmentally friendly catalyst, an enzyme lipase. The third laboratory activity challenged students to design their own experiments to synthesize other esters using lipase-catalyzed esterification reactions. At the end of the learning unit, students in each group presented the results and conclusions of the third laboratory activity to the whole class and explained how the 12 principles of green chemistry were applied in the laboratory. The results from the Learning Unit Conceptual Test and Learning Unit Perceptions Questionnaire indicate that the learning units can promote students conceptual understanding. They also have positive perceptions toward green chemistry and learning units.