Background: Many stakeholders recognise the importance of integrated STEM education in nurturing 21st century skills but little consideration has been given to how scientific creativity can be fostered through this approach among young learners. Purpose and Methods: The study describes the classroom experience of incorporating three authentic design-based STEM projects (1. Development of a Disinfection Device, 2. Building an Intelligent Transportation Model, and 3. Design an Ecologically Smart Pond) of grades five and six primary students and illustrates how the activities integrated different STEM disciplines. Descriptions of the projects’ three design-based integrated activities, lasting 12–16 weeks, were developed by three primary STEM teachers from three different schools in Macau, each of whom had at least two years of experience in implementing STEM learning. This is a mixed method research where semi-structured interviews with the teachers revealed how they fostered students’ scientific creativity through design and how the incorporation of the design process stimulated their scientific creativity. The effects of the activities on scientific creativity development, on the other hands, were quantitatively compared for 120 students who participated in STEM projects and a control group of 120 students who were not from the three schools. Result: The findings revealed that teachers foster scientific creativity of students throughout the design process and students who participated in the project exhibited significantly higher scientific creativity, particularly in dimensions related to design. Conclusion: Hence, the engineering design process is an effective instructional approach for supporting cross-disciplinary STEM learning in primary grades as well as nurturing scientific inquiry and fostering students’ scientific creativity.