This study aims to review the implementation of a project-based laboratory in a natural product chemistry course in order to isolate secondary metabolites from medicinal plants. Various studies on the isolation and structure elucidation of secondary metabolites can be used in natural products laboratory project. Students are directed to study literature related to secondary metabolites isolation and structure elucidation procedures. Furthermore, students practice skills of extraction, fractionation, purification, and structure elucidation of secondary metabolites. Once students have an understanding of secondary metabolites isolation and structure elucidation procedure, they were asked to design the isolation procedure of secondary metabolites. In addition, students implemented their own design to isolate secondary metabolites. This study used a quasi-experimental research. Data was collected done through observation and qualitatively analysis was conducted on the collected data. Participants in this study comprised 32 third-year students from the chemistry education department at one of the state universities in West Nusa Tenggara, Indonesia. Participants were divided into eight groups. Each group worked on one plant sample that comprised roots of "Artocarpus heterophyllus," fruit of "Piper nigrum," rhizome of "Curcuma xanthorrhiza," rhizome of "Kaempferia pandurata," rhizome of "Curcuma aeruginosa," rhizome of "Kaempferia galanga," fruit of "Cassia grandis," and seeds of "Cassia grandis." In this laboratory project, two groups succeeded in structural elucidation of their isolated secondary metabolites, piperin (1) from "Piper nigrum" and andrographolide (2) from "Andrographis paniculata."