Students who are innovating in a project-based context need appropriate frameworks to support applied research that is easily understandable, flexible to different contexts, and appropriate to their needs. Such support is particularly important when the research involves the development of a technology-related artifact, where students need empirical methods for the design and evaluation of that artifact, in addition to guidance in meeting the academic requirements of their courses. This chapter describes a Scrum-based approach for supporting innovations in learning contexts, extending previous proposals in the literature. The context of the research is two academic programs where students undertake innovative technology-based research projects. The new research model is designed to provide a better supporting framework to assist them to effectively manage their projects by integrating the adaptive cycles and ceremonies of the Scrum agile method with complementary concepts and phases from Design Thinking, Design Science, and Design-Based Research.