Research-based pedagogy was implemented to enhance high school students' learning outcomes in basic organic chemistry. Flipped learning and structured peer work have been offered to grade 10 students(N = 12) during the course with appropriate classroom facilities, supervised by two facilitators. The preclass and in-class activities were designed based on the principles of the flipped pedagogy and combined with structured peer work to improve chemistry learning outcomes among students. The successful implementation of this pedagogical approach helped students to overcome misconceptions, improve conceptual understanding, and build confidence in learning organic chemistry. The hands-on experiments were also carried out by students in a well-equipped laboratory to learn about the synthesis and properties of organic compounds. In addition, the paper presents the assessments of students' performances conducted before and after structured peer work sessions to understand the effectiveness of merging collaborative learning with a flipped classroom framework. The students' learning outcomes were evaluated using a combination of qualitative and quantitative methods, specifically employing the Three-Dimensional Learning Assessment Protocol (3D LAP). The study results showed that the collaborative activities by structured peer work boosted the students' learning outcomes in the flipped organic chemistry course, and this improvement was statistically significant (examined by t-test, p-value = 0.0001). The feedback from the students regarding this course reflected a positive response and their favorable perspective on it. Herein, we provide the detailed methodology and the student's learning materials with the required instructions to conduct a basic organic chemistry course at the high school level.