This study investigates the impact of Augmented Reality (AR) on STEM education by examining its influence on student engagement, comprehension, and motivation. Utilizing the AR 4 STEM mobile app for a theoretical Microbial Photosynthetic Electricity Generation (MPEG) STEM kit, 160 Malaysian secondary school students explored complex scientific concepts through interactive AR experiences. The technology facilitated hands-on learning, allowing students to visualize biochemical processes and bridge theoretical knowledge with real-world applications. Pre- and post-intervention surveys revealed significant improvements in students’ interest, confidence, and understanding of STEM topics, underscoring AR’s potential to enhance learning in challenging STEM domains. Despite these positive results, challenges related to device compatibility, and instructional clarity highlighted areas for further improvements. This research concludes that AR holds transformative potential for STEM education, offering a dynamic, interdisciplinary platform that fosters deep learning and sustained interest in science and technology fields.