This paper explores the qualitative impact of the Integrated Online Problem-Based Learning (iON-PBL) Module of Physics on pre-university students’ motivation and problem-solving skills. The iON-PBL module, developed with ADDIE instructional design, addresses self-efficacy, intrinsic value, cognitive strategies, and self-regulation. Data from focus group interviews highlight improvements in students’ confidence, engagement, and collaborative problem-solving. However, challenges such as dependency on group support, difficulty with open-ended problems, and reduced motivation were highlighted. The findings suggest that iON-PBL bridges traditional and modern pedagogies, enhancing STEM education’s inclusivity and adaptability. The study also emphasizes the need for effective design and strategies to overcome barriers to independent learning, contributing to the integration of constructivism and connectivism in STEM education.