Organic chemistry education serves as a cornerstone in various scientific disciplines, yet its instruction is often dominated by rote memorization over deep conceptual understanding, resulting in limited conceptual understanding and disengagement among students. This aimed at investigating the impact of integrating a web-based discussion tools on students' conceptual understanding and 21st century skills development in organic chemistry education. The study randomly sampled 343 secondary including 229 senior two and 114 senior five from Kamonyi and Gasabo districts, Rwanda. The research adopted a quasi-experimental research design. The existing intact classes were assigned to either the control which engaged in traditional group discussions or experimental group which utilized structured web-based discussion tools. The data were collected through pre- and post-intervention tests and questionnaires assessing both conceptual understanding and 21st century skills development, respectively. Descriptive and inferential statistical analyses, including Multivariate Analysis of Variance (MANOVA) and Pearson correlation were used to analyze the collected data. The Results revealed a substantial improvement in both students' conceptual understanding and 21st century skills development in organic chemistry concepts in favor of post-intervention, particularly among those engaged in a web-based discussion tools (p < 0.001), respectively. The main skills developed include adaptability, teamwork, communication, time management, resourcefulness, dependability, and self-motivation. In addition, a strong positive correlation was also observed between conceptual understanding and skill acquisition. These findings underscore the effectiveness of web-based discussion tools in fostering deeper learning and twenty-first century skills. Therefore, this study provides valuable insights into the role of pedagogical innovation in science education and emphasizes the need for widespread adoption of digital learning tools in secondary school curricula.